Identification of cancer-cytotoxic modulators of PDE3A by predictive chemogenomics

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Abstract

High cancer death rates indicate the need for new anticancer therapeutic agents. Approaches to discovering new cancer drugs include target-based drug discovery and phenotypic screening. Here, we identified phosphodiesterase 3A modulators as cell-selective cancer cytotoxic compounds through phenotypic compound library screening and target deconvolution by predictive chemogenomics. We found that sensitivity to 6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2H)-one, or DNMDP, across 766 cancer cell lines correlates with expression of the gene PDE3A, encoding phosphodiesterase 3A. Like DNMDP, a subset of known PDE3A inhibitors kill selected cancer cells, whereas others do not. Furthermore, PDE3A depletion leads to DNMDP resistance. We demonstrated that DNMDP binding to PDE3A promotes an interaction between PDE3A and Schlafen 12 (SLFN12), suggestive of a neomorphic activity. Coexpression of SLFN12 with PDE3A correlates with DNMDP sensitivity, whereas depletion of SLFN12 results in decreased DNMDP sensitivity. Our results implicate PDE3A modulators as candidate cancer therapeutic agents and demonstrate the power of predictive chemogenomics in small-molecule discovery.

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Figure 1: Identification and characterization of DNMDP, a potent and selective cancer cell cytotoxic agent.
Figure 2: PDE3A expression correlates with sensitivity to DNMDP, but inhibition of PDE3A-mediated cAMP hydrolysis does not correlate with cytotoxicity.
Figure 3: Nonlethal PDE3 inhibitors rescue cell death induced by DNMDP by competing for the binding of PDE3A.
Figure 4: PDE3A is not essential in sensitive cell lines but is required for relaying the cytotoxic signal.
Figure 5: PDE3A immunoprecipitation in the presence of DNMDP reveals novel SIRT7 and SLFN12 interaction.
Figure 6: Cell lines with dual expression of SLFN12 and PDE3A are significantly enriched for DNMDP-sensitive cell lines.

Change history

  • 22 December 2015

    In the version of this article initially published, there was a typographical error in the Additional Information section that switched H.G. to H.H. The error has been corrected in the print, HTML and PDF versions of the article.

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Acknowledgements

This work was supported in part by the US National Cancer Institute (NCI) Grant (grant number 1R35CA197568, awarded to M.M.), the American Cancer Society Research Professorship (awarded to M.M.), the Doctors Cancer Foundation (awarded to H.G.), the Friends of Dana-Farber Cancer Institute (awarded to H.G.), and the US National Institutes of Health's Molecular Libraries Program Center Network (MLPCN) (grant number 3U54HG005032-05S1, awarded to H.G., M.M. and S.L.S.). The cancer cell-line profiling studies were supported in part by the NCI's Cancer Target Discovery and Development (CTD2) Network (grant number U01CA176152, awarded to S.L.S.). We thank A. Bhatt, H. Gannon, J. Jung, T. Sharifnia and all members of the Meyerson laboratory for their advice and helpful discussions. S.L.S. is an Investigator of the Howard Hughes Medical Institute.

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Contributions

L.d.W., P.W.F., M.J.H., N.T., A.N.K., H.G. and M.M. designed and performed the phenotypic small-molecule screen. M.G.R., A.T., P.A.C., A.F.S. and S.L.S. designed and performed experiments identifying PDE3A expression correlation with DNMDP sensitivity. L.d.W., T.A.L., L.G., B.K.W., B.M. and H.G. designed and performed experiments demonstrating physical interaction of DNMDP with PDE3A and rescue phenotype by non-cytotoxic PDE3 inhibitors. L.d.W., P.S.C., H.G. and M.M. designed and performed PDE3A protein level reduction leading to DNMDP resistance. L.d.W., X.W., C.H., S.A.C., M.S., A.B.B., H.G. and M.M. designed and performed PDE3A immunoprecipitation experiment revealing novel protein-protein interaction partners facilitated by DNMDP binding. L.d.W., X.W., M.G.R., A.T., H.G. and M.M. designed and performed experiments showing requirement of SLFN12 for DNMDP phenotype and genomic correlation with DNMDP sensitivity. L.d.W. made the figures, and L.d.W., T.A.L., H.G. and M.M. wrote the manuscript.

Corresponding authors

Correspondence to Heidi Greulich or Matthew Meyerson.

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Competing interests

L.d.W., T.A.L., X.W., P.A.C., S.L.S., H.G. and M.M. receive research support from Bayer. M.M. is a founder, consultant and equity holder in Foundation Medicine. L.d.W., T.A.L., L.G., B.M., H.G. and M.M. are inventors on patent WO 2014/164704 A2, covering the chemical space around DNMDP and some of the analogs described in the supplementary information.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–11, Supplementary Tables 1–6 and Supplementary Note. (PDF 2030 kb)

Supplementary Dataset 1

Screening data of 1924 compounds in A549 and NCI-H1734 (XLSX 293 kb)

Supplementary Dataset 2

Sensitivity data of 766 cancer cell lines treated with DNMDP (XLSX 70 kb)

Supplementary Dataset 3

Results from competition screen using 1600 bioactive compounds to rescue DNMDP cytotoxicity in the HeLa cell line. (XLSX 135 kb)

Supplementary Dataset 4

Results from PDE3A immunoprecipitation followed by iTRAQ/MS in the presence of blocking peptide, DMSO, DNMDP and trequinsin. (XLSX 1345 kb)

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de Waal, L., Lewis, T., Rees, M. et al. Identification of cancer-cytotoxic modulators of PDE3A by predictive chemogenomics. Nat Chem Biol 12, 102–108 (2016). https://doi.org/10.1038/nchembio.1984

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