Abstract

Plasticity of the cell state has been proposed to drive resistance to multiple classes of cancer therapies, thereby limiting their effectiveness1,2,3,4. A high-mesenchymal cell state observed in human tumours and cancer cell lines has been associated with resistance to multiple treatment modalities across diverse cancer lineages, but the mechanistic underpinning for this state has remained incompletely understood1,2,3,4,5,6. Here we molecularly characterize this therapy-resistant high-mesenchymal cell state in human cancer cell lines and organoids and show that it depends on a druggable lipid-peroxidase pathway that protects against ferroptosis, a non-apoptotic form of cell death induced by the build-up of toxic lipid peroxides7,8. We show that this cell state is characterized by activity of enzymes that promote the synthesis of polyunsaturated lipids. These lipids are the substrates for lipid peroxidation by lipoxygenase enzymes8,9. This lipid metabolism creates a dependency on pathways converging on the phospholipid glutathione peroxidase (GPX4), a selenocysteine-containing enzyme that dissipates lipid peroxides and thereby prevents the iron-mediated reactions of peroxides that induce ferroptotic cell death8. Dependency on GPX4 was found to exist across diverse therapy-resistant states characterized by high expression of ZEB1, including epithelial–mesenchymal transition in epithelial-derived carcinomas, TGFβ-mediated therapy-resistance in melanoma, treatment-induced neuroendocrine transdifferentiation in prostate cancer, and sarcomas, which are fixed in a mesenchymal state owing to their cells of origin. We identify vulnerability to ferroptic cell death induced by inhibition of a lipid peroxidase pathway as a feature of therapy-resistant cancer cells across diverse mesenchymal cell-state contexts.

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Acknowledgements

We thank M. J. Hangauer, M. T. McManus, F. McCormick, K. Dutton-Regester, L. V. Kemeny, D. J. Adams and Y. Drier for valuable discussions and L. Hartman for execution of in vivo studies. This project has been supported by grants from the National Cancer Institute (Cancer Target Discovery and Development Network grant U01CA176152 to S.L.S., U01CA168397 to M.E.B., 5R01CA097061 and R01CA161061 to B.R.S., NCI-CA129933 to D.A.H., P30CA008748 to Y.C.), the National Institutes of Health (R01GM038627 to S.L.S., 5R01GM085081 to B.R.S.), the Swiss National Fund (310030_149946, to M.P.L.) and Howard Hughes Medical Institute (D.A.H., S.L.S.).

Author information

Affiliations

  1. Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA

    • Vasanthi S. Viswanathan
    • , Matthew J. Ryan
    • , Shubhroz Gill
    • , Brinton Seashore-Ludlow
    • , John K. Eaton
    • , Andrew J. Aguirre
    • , Srinivas R. Viswanathan
    • , Shrikanta Chattopadhyay
    • , Pablo Tamayo
    • , Matthew G. Rees
    • , Sixun Chen
    • , Zarko V. Boskovic
    • , Cherrie Huang
    • , Xiaoyun Wu
    • , Yuen-Yi Tseng
    • , Jill P. Mesirov
    • , Jesse S. Boehm
    • , Joanne D. Kotz
    • , Cindy S. Hon
    • , William C. Hahn
    • , John G. Doench
    • , Alykhan F. Shamji
    • , Paul A. Clemons
    •  & Stuart L. Schreiber
  2. Cancer and Cell Biology Division, The Translational Genomics Research Institute, 445 N 5th Street, Phoenix, Arizona 85004, USA

    • Harshil D. Dhruv
    •  & Michael E. Berens
  3. Department of Dermatology, University of Zurich, University Hospital of Zurich, Wagistrasse 14, CH-8952, Schlieren, Zürich, Switzerland

    • Ossia M. Eichhoff
    • , Elisabeth M. Roider
    •  & Mitchell P. Levesque
  4. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA

    • Samuel D. Kaffenberger
    • , Dong Gao
    •  & Yu Chen
  5. Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA

    • Kenichi Shimada
  6. Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA

    • Andrew J. Aguirre
    • , Srinivas R. Viswanathan
    • , James M. Cleary
    • , Brian M. Wolpin
    •  & William C. Hahn
  7. Moores Cancer Center & Department of Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093, USA

    • Pablo Tamayo
    •  & Jill P. Mesirov
  8. Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439, USA

    • Wan Seok Yang
  9. Massachusetts General Hospital Cancer Center, 149 13th Street, Charlestown, Massachusetts 02129, USA

    • Sarah Javaid
    •  & Daniel A. Haber
  10. Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA

    • Daniel A. Haber
    •  & Stuart L. Schreiber
  11. Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, Massachusetts 02139, USA

    • Jeffrey A. Engelman
  12. Department of Biological Sciences, Department of Chemistry, Columbia University, 550 West 120th Street, New York, New York 10027, USA

    • Brent R. Stockwell
  13. Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, USA

    • Stuart L. Schreiber

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Contributions

S.L.S. directed the project; S.L.S. and V.S.V. wrote the manuscript; V.S.V. and M.J.R. performed research; H.D.D. performed in vivo experiments; S.G. performed CRISPR experiments; O.M.E. performed TGFβ treatment of melanoma cell lines; S.R.V. and S.Che. generated CRISPR reagents; S.D.K. performed organoid experiments; B.S.-L., A.J.A., M.G.R. and P.T. generated mesenchymal scores; K.S. performed the lipid peroxidation assay; W.S.Y. performed the GPX4 activity assay; Z.V.B. and J.K.E synthesized compounds; S.Cha. and C.H. contributed to profiling of non-transformed cell lines; J.M.C. and B.M.W. collected patient samples; A.J.A., X.W. and Y.-Y.T. generated patient-derived pancreatic cancer cell lines; J.P.M., D.A.H., J.A.E., J.S.B., D.G., S.J., Y.C., W.C.H., M.P.L., J.G.D., E.M.R and M.E.B. contributed reagents; J.D.K., C.S.H., B.R.S. and A.F.S. provided project support; P.A.C. oversaw data analysis; V.S.V. and P.A.C. performed large-scale data analysis.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Stuart L. Schreiber.

Reviewer Information Nature thanks N. Chandel, T. Sato and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Data

    This file contains raw western blot files for extended data figures 1, 2c, 7a and 7b.

Excel files

  1. 1.

    Supplementary Table 1

    This table contains mesenchymal scores for 516 carcinoma-derived cell lines calculated using single-sample gene set enrichment analysis from Taube, Goger and Byers EMT gene sets.

  2. 2.

    Supplementary Table 2

    This table contains mesenchymal score-correlations for 481 compounds computed from AUCs across 491 carcinoma-derived cell lines listed in Supplementary Table 1.

  3. 3.

    Supplementary Table 3

    This table contains gene-expression data for MCF-7 ER-Snail-1 cells (Haber Lab) treated with 4-hydroxytamoxifen (4-OHT) for 120 hours, allowed to recover from 4-OHT treatment for 24 hours, and then cultured in 384-well format in the absence of 4-OHT for 96 hours. These conditions model the compound exposure conditions for 4-OHT-induced MCF-7 ER-Snail-1 cells shown in Extended Data Fig. 6. Data are shown relative to ethanol-treated control cells.

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DOI

https://doi.org/10.1038/nature23007

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