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Mode of action and pharmacogenomic biomarkers for exceptional responders to didemnin B

Abstract

Modern cancer treatment employs many effective chemotherapeutic agents originally discovered from natural sources. The cyclic depsipeptide didemnin B has demonstrated impressive anticancer activity in preclinical models. Clinical use has been approved but is limited by sparse patient responses combined with toxicity risk and an unclear mechanism of action. From a broad-scale effort to match antineoplastic natural products to their cellular activities, we found that didemnin B selectively induces rapid and wholesale apoptosis through dual inhibition of PPT1 and EEF1A1. Furthermore, empirical discovery of a small panel of exceptional responders to didemnin B allowed the generation of a regularized regression model to extract a sparse-feature genetic biomarker capable of predicting sensitivity to didemnin B. This may facilitate patient selection in a fashion that could enhance and expand the therapeutic application of didemnin B against neoplastic disease.

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Figure 1: Natural-product FUSION identifies didemnin B as an activator of mTORC1.
Figure 2: An exceptional responder reveals context-specific induction of apoptosis by didemnin B.
Figure 3: Combinatorial inhibition of PPT1 and protein synthesis recapitulates selective induction of apoptosis by didemnin B.
Figure 4: A subset of breast, colon and lung cancer cell lines are selectively sensitive to didemnin B.
Figure 5: Molecular response predictor for exceptional sensitivity to didemnin B.
Figure 6: Predictive power in hematological cancer.

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References

  1. Newman, D.J. & Cragg, G.M. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J. Nat. Prod. 75, 311–335 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Potts, M.B. et al. Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Sci. Signal. 6, ra90 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Hu, Y. et al. Discoipyrroles A-D: isolation, structure determination, and synthesis of potent migration inhibitors from Bacillus hunanensis. J. Am. Chem. Soc. 135, 13387–13392 (2013).

    Article  CAS  PubMed  Google Scholar 

  4. Rinehart, K.L. Jr. et al. Didemnins: antiviral and antitumor depsipeptides from a Caribbean tunicate. Science 212, 933–935 (1981).

    Article  CAS  PubMed  Google Scholar 

  5. Rinehart, K.L. Jr., Gloer, J.B., Cook, J.C. Jr., Mizsak, S.A. & Scahill, T.A. Structures of the didemnins, antiviral and cytotoxic depsipeptides from a Caribbean tunicate. J. Am. Chem. Soc. 103, 1857–1859 (1981).

    Article  CAS  Google Scholar 

  6. Lee, J., Currano, J.N., Carroll, P.J. & Joullie, M.M. Didemnins, tamandarins and related natural products. Nat. Prod. Rep. 29, 404–424 (2012).

    Article  CAS  PubMed  Google Scholar 

  7. Le Tourneau, C., Raymond, E. & Faivre, S. Aplidine: a paradigm of how to handle the activity and toxicity of a novel marine anticancer poison. Curr. Pharm. Des. 13, 3427–3439 (2007).

    Article  CAS  PubMed  Google Scholar 

  8. Vera, M.D. & Joullie, M.M. Natural products as probes of cell biology: 20 years of didemnin research. Med. Res. Rev. 22, 102–145 (2002).

    Article  CAS  PubMed  Google Scholar 

  9. Fritz, R.D., Varga, Z. & Radziwill, G. CNK1 is a novel Akt interaction partner that promotes cell proliferation through the Akt-FoxO signalling axis. Oncogene 29, 3575–3582 (2010).

    Article  CAS  PubMed  Google Scholar 

  10. Lim, J., Zhou, M., Veenstra, T.D. & Morrison, D.K. The CNK1 scaffold binds cytohesins and promotes insulin pathway signaling. Genes Dev. 24, 1496–1506 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Sridharan, S. & Basu, A. S6 kinase 2 promotes breast cancer cell survival via Akt. Cancer Res. 71, 2590–2599 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Katayama, K., Fujita, N. & Tsuruo, T. Akt/protein kinase B-dependent phosphorylation and inactivation of WEE1Hu promote cell cycle progression at G2/M transition. Mol. Cell. Biol. 25, 5725–5737 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kaul, G., Pattan, G. & Rafeequi, T. Eukaryotic elongation factor-2 (eEF2): its regulation and peptide chain elongation. Cell Biochem. Funct. 29, 227–234 (2011).

    Article  CAS  PubMed  Google Scholar 

  14. Kefas, B. et al. microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. Cancer Res. 68, 3566–3572 (2008).

    Article  CAS  PubMed  Google Scholar 

  15. Li, Z.Y., Na, H.M., Peng, G., Pu, J. & Liu, P. Alteration of microRNA expression correlates to fatty acid-mediated insulin resistance in mouse myoblasts. Mol. Biosyst. 7, 871–877 (2011).

    Article  CAS  PubMed  Google Scholar 

  16. Creevey, L. et al. MicroRNA-497 increases apoptosis in MYCN amplified neuroblastoma cells by targeting the key cell cycle regulator WEE1. Mol. Cancer 12, 23 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Guo, S.T. et al. MicroRNA-497 targets insulin-like growth factor 1 receptor and has a tumour suppressive role in human colorectal cancer. Oncogene 32, 1910–1920 (2013).

    Article  CAS  PubMed  Google Scholar 

  18. He, Z. et al. Downregulation of miR-383 promotes glioma cell invasion by targeting insulin-like growth factor 1 receptor. Med. Oncol. 30, 557 (2013).

    Article  PubMed  CAS  Google Scholar 

  19. Gong, J.N. et al. The role, mechanism and potentially therapeutic application of microRNA-29 family in acute myeloid leukemia. Cell Death Differ. 21, 100–112 (2014).

    Article  CAS  PubMed  Google Scholar 

  20. Li, Y. et al. Epigenetic silencing of microRNA-193a contributes to leukemogenesis in t(8;21) acute myeloid leukemia by activating the PTEN/PI3K signal pathway. Blood 121, 499–509 (2013).

    Article  CAS  PubMed  Google Scholar 

  21. Shah, O.J., Wang, Z. & Hunter, T. Inappropriate activation of the TSC/Rheb/mTOR/S6K cassette induces IRS1/2 depletion, insulin resistance, and cell survival deficiencies. Curr. Biol. 14, 1650–1656 (2004).

    Article  CAS  PubMed  Google Scholar 

  22. Briaud, I. et al. Insulin receptor substrate-2 proteasomal degradation mediated by a mammalian target of rapamycin (mTOR)-induced negative feedback down-regulates protein kinase B-mediated signaling pathway in beta-cells. J. Biol. Chem. 280, 2282–2293 (2005).

    Article  CAS  PubMed  Google Scholar 

  23. Hsu, P.P. et al. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 332, 1317–1322 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yu, Y. et al. Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science 332, 1322–1326 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Crews, C.M., Collins, J.L., Lane, W.S., Snapper, M.L. & Schreiber, S.L. GTP-dependent binding of the antiproliferative agent didemnin to elongation factor 1 alpha. J. Biol. Chem. 269, 15411–15414 (1994).

    Article  CAS  PubMed  Google Scholar 

  26. Crews, C.M., Lane, W.S. & Schreiber, S.L. Didemnin binds to the protein palmitoyl thioesterase responsible for infantile neuronal ceroid lipofuscinosis. Proc. Natl. Acad. Sci. USA 93, 4316–4319 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. SirDeshpande, B.V. & Toogood, P.L. Mechanism of protein synthesis inhibition by didemnin B in vitro. Biochemistry 34, 9177–9184 (1995).

    Article  CAS  PubMed  Google Scholar 

  28. Meng, L., Sin, N. & Crews, C.M. The antiproliferative agent didemnin B uncompetitively inhibits palmitoyl protein thioesterase. Biochemistry 37, 10488–10492 (1998).

    Article  CAS  PubMed  Google Scholar 

  29. Das, A.K. et al. Structural basis for the insensitivity of a serine enzyme (palmitoyl-protein thioesterase) to phenylmethylsulfonyl fluoride. J. Biol. Chem. 275, 23847–23851 (2000).

    Article  CAS  PubMed  Google Scholar 

  30. Blenis, J., Chung, J., Erikson, E., Alcorta, D.A. & Erikson, R.L. Distinct mechanisms for the activation of the RSK kinases/MAP2 kinase/pp90rsk and pp70–S6 kinase signaling systems are indicated by inhibition of protein synthesis. Cell Growth Differ. 2, 279–285 (1991).

    CAS  PubMed  Google Scholar 

  31. Kimball, S.R., Do, A.N., Kutzler, L., Cavener, D.R. & Jefferson, L.S. Rapid turnover of the mTOR complex 1 (mTORC1) repressor REDD1 and activation of mTORC1 signaling following inhibition of protein synthesis. J. Biol. Chem. 283, 3465–3475 (2008).

    Article  CAS  PubMed  Google Scholar 

  32. Terada, N. et al. Rapamycin selectively inhibits translation of mRNAs encoding elongation factors and ribosomal proteins. Proc. Natl. Acad. Sci. USA 91, 11477–11481 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gupta, P. et al. Disruption of PPT1 or PPT2 causes neuronal ceroid lipofuscinosis in knockout mice. Proc. Natl. Acad. Sci. USA 98, 13566–13571 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Voznyi, Y.V. et al. A new simple enzyme assay for pre- and postnatal diagnosis of infantile neuronal ceroid lipofuscinosis (INCL) and its variants. J. Med. Genet. 36, 471–474 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Pajic, A. et al. Cell cycle activation by c-myc in a Burkitt lymphoma model cell line. Int. J. Cancer 87, 787–793 (2000).

    Article  CAS  PubMed  Google Scholar 

  36. Grubb, D.R., Wolvetang, E.J. & Lawen, A. Didemnin B induces cell death by apoptosis: the fastest induction of apoptosis ever described. Biochem. Biophys. Res. Commun. 215, 1130–1136 (1995).

    Article  CAS  PubMed  Google Scholar 

  37. Collins, S. & Groudine, M. Amplification of endogenous myc-related DNA sequences in a human myeloid leukaemia cell line. Nature 298, 679–681 (1982).

    Article  CAS  PubMed  Google Scholar 

  38. Leary, R.J. et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc. Natl. Acad. Sci. USA 105, 16224–16229 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Zou, H. & Hastie, T. Regularization and variable selection via the elastic net. J. R. Stat. Soc., B 67, 301–320 (2005).

    Article  Google Scholar 

  41. Savukoski, M. et al. Defined chromosomal assignment of CLN5 demonstrates that at least four genetic loci are involved in the pathogenesis of human ceroid lipofuscinoses. Am. J. Hum. Genet. 55, 695–701 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Mamo, A., Jules, F., Dumaresq-Doiron, K., Costantino, S. & Lefrancois, S. The role of ceroid lipofuscinosis neuronal protein 5 (CLN5) in endosomal sorting. Mol. Cell. Biol. 32, 1855–1866 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Soares, D.C. & Abbott, C.M. Highly homologous eEF1A1 and eEF1A2 exhibit differential post-translational modification with significant enrichment around localised sites of sequence variation. Biol. Direct 8, 29 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Stumpf, C.R. & Ruggero, D. The cancerous translation apparatus. Curr. Opin. Genet. Dev. 21, 474–483 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Ribrag, V. et al. Multicenter phase II study of plitidepsin in patients with relapsed/refractory non-Hodgkin′s lymphoma. Haematologica 98, 357–363 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Suryani, S. et al. Cell and molecular determinants of in vivo efficacy of the BH3 mimetic ABT-263 against pediatric acute lymphoblastic leukemia xenografts. Clin. Cancer Res. 20, 4520–4531 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Belmar, J. & Fesik, S.W. Small molecule Mcl-1 inhibitors for the treatment of cancer. Pharmacol. Ther. 145, 76–84 (2015).

    Article  CAS  PubMed  Google Scholar 

  48. Robinson, D.R. et al. Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat. Med. 17, 1646–1651 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Gazdar, A.F. et al. Characterization of paired tumor and non-tumor cell lines established from patients with breast cancer. Int. J. Cancer 78, 766–774 (1998).

    Article  CAS  PubMed  Google Scholar 

  50. Hackett, A.J. et al. Two syngeneic cell lines from human breast tissue: the aneuploid mammary epithelial (Hs578T) and the diploid myoepithelial (Hs578Bst) cell lines. J. Natl. Cancer Inst. 58, 1795–1806 (1977).

    Article  CAS  PubMed  Google Scholar 

  51. Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006).

    Article  CAS  PubMed  Google Scholar 

  52. Gazdar, A.F., Girard, L., Lockwood, W.W., Lam, W.L. & Minna, J.D. Lung cancer cell lines as tools for biomedical discovery and research. J. Natl. Cancer Inst. 102, 1310–1321 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Klionsky, D.J. et al. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 4, 151–175 (2008).

    Article  CAS  PubMed  Google Scholar 

  54. Tsukimoto, M. et al. Bacterial production of the tunicate-derived antitumor cyclic depsipeptide didemnin B. J. Nat. Prod. 74, 2329–2331 (2011).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank T. Molinski for providing additional Trididemnum solidum material; D. Sabatini and N. Gray for the Torin1; J. Willson and S. Markowitz for the Vaco colon cancer cell lines; K. Huffman, M. Peyton, A. Gazdar and J. Minna for the lung and breast cancer cell lines; J. Shay for the human colonic epithelial cells; X. Wang for the U2OS GFP-LC3 cells; J. Brugarolas for the REDD1-knockout MEFs; F. Grinnell for the BR5 fibroblasts; R. Potts for the U2OS cells and J. Mendell for the P493 cells. We also thank N. Williams for formulating didemnin B for animal delivery. This study was supported by the Welch Foundation (I-1414, I-1689), the US National Cancer Institute (CA071443, CA176284, CA149833) and the Cancer Prevention and Research Institute of Texas (RP120718, RP110708). M.B.P. was supported by a Komen for the Cure Postdoctoral Fellowship. E.A.M. was supported in part by the US National Institutes of Health (2T32GM008203). Y.-H.O. and H.S.K. were supported by fellowships from the Cancer Interventions and Discoveries Program (RP101496).

Author information

Authors and Affiliations

Authors

Contributions

J.B.M. produced UT-BA07-004-ETOAC, purified didemnin B and solved its structure. M.B.P., H.S.K. and M.A.W. performed the analyses that led to the prediction that UT-BA07-004-ETOAC may inhibit AKT signaling. M.B.P., T.I.R. and Y.-H.O. performed the experiments that confirmed this prediction and elucidated the underlying mechanism. R.A.B., J.E.T. and M.B.P. designed and performed the mouse experiment. M.B.P. and T.I.R. identified cancer cell lines exhibiting exceptional sensitivity to didemnin B and determined the underlying mechanism. E.A.M. performed the elastic net analysis and the biomarker-based prediction analyses, and T.I.R. and M.B.P. tested the resulting predictions experimentally. M.D.M. provided the OCI cell lines. M.A.W. supervised the research. M.B.P. and M.A.W. wrote the manuscript.

Corresponding author

Correspondence to Michael A White.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–6 and full gels. (PDF 44093 kb)

Supplementary Data Set 1

Biomarker predictions and cell line information corresponding to Figure 5b. (XLSX 61 kb)

Supplementary Data Set 2

Biomarker predictions and patient sample information corresponding to Figure 5c and Supplementary Figure 5a and b. (XLSX 286 kb)

Supplementary Data Set 3

Most differentially expressed genes between didemnin B sensitive and didemnin B resistant cell lines, as determined by S2N analysis, corresponding to Figure 6a-c and Supplementary Figure 6a. (XLSX 87 kb)

Supplementary Data Set 4

Gene sets significantly enriched in didemnin B resistant vs. sensitive class. (XLSX 13 kb)

Supplementary Data Set 5

Gene sets significantly enriched in didemnin B sensitive vs. resistant class. (XLSX 11 kb)

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Potts, M., McMillan, E., Rosales, T. et al. Mode of action and pharmacogenomic biomarkers for exceptional responders to didemnin B. Nat Chem Biol 11, 401–408 (2015). https://doi.org/10.1038/nchembio.1797

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