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Abstract

Cancer cells develop mechanisms to escape immunosurveillance, among which modulating the expression of immune suppressive messenger RNAs is most well-documented. However, how this is molecularly achieved remains largely unresolved. Here, we develop an in vivo mouse model of liver cancer to study oncogene cooperation in immunosurveillance. We show that MYC overexpression (MYCTg) synergizes with KRASG12D to induce an aggressive liver tumor leading to metastasis formation and reduced mouse survival compared with KRASG12D alone. Genome-wide ribosomal footprinting of MYCTg;KRASG12 tumors compared with KRASG12D revealed potential alterations in translation of mRNAs, including programmed-death-ligand 1 (PD-L1). Further analysis revealed that PD-L1 translation is repressed in KRASG12D tumors by functional, non-canonical upstream open reading frames in its 5′ untranslated region, which is bypassed in MYCTg;KRASG12D tumors to evade immune attack. We show that this mechanism of PD-L1 translational upregulation was effectively targeted by a potent, clinical compound that inhibits eIF4E phosphorylation, eFT508, which reverses the aggressive and metastatic characteristics of MYCTg;KRASG12D tumors. Together, these studies reveal how immune-checkpoint proteins are manipulated by distinct oncogenes at the level of mRNA translation, which can be exploited for new immunotherapies.

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The sequencing data of the manuscript can be accessed using the following accession number: GSE105147.

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Acknowledgements

We would like to thank members of the Ruggero laboratory for discussion and critical reading of the manuscript. We thank C. Her for his help with the mouse HCC cell line generation protocol, D. Wang for the help with hydrodynamic transfection, and K. Fujii and D. Simsek for advice and technique assistance. We thank B. Tiano for the contribution in developing and characterizing the MYC transgenic mice. This work was supported by the Damon Runyon Postdoctoral Fellowship (Y.X.), AACR-Incyte Corporation Fellowship In Basic Cancer Research (grant no. 17-40-46-JIN) (H.Y.J), Life Science Foundation Postdoctoral Fellowship (S.Z.), Department of Defense Physician training award (H.G.N), the Campini Foundation, The Leukemia and Lymphoma Foundation Career Development Grant and UCSF Department of Pediatrics K12 (grant no. 5K12HDO72222-05) (C.M.F.), American Cancer Society Postdoctoral Fellowship and Conquer Cancer Foundation Young Investigator Award (J.D.G), Pew Scholars Award (M.B.), NIH grant no. 1R01HD086634 (M.B.), NIH grants (nos. R01CA140456, R01CA154916, and R01CA184624) (D.R.). M.B. is a New York Stem Cell Foundation Robertson Investigator. D.R. is a Leukemia and Lymphoma Society Scholar.

Author information

Author notes

  1. These authors contributed equally: Yichen Xu and Mauro Poggio.

Affiliations

  1. Department of Urology, University of California, San Francisco, San Francisco, CA, USA

    • Yichen Xu
    • , Mauro Poggio
    • , Hyun Yong Jin
    • , Craig M. Forester
    • , Ying Wang
    • , Craig R. Stumpf
    • , Lingru Xue
    • , Emily Devericks
    • , Lomon So
    • , Hao G. Nguyen
    • , Alice Griselin
    • , John T. Cunningham
    •  & Davide Ruggero
  2. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA

    • Yichen Xu
    • , Mauro Poggio
    • , Hyun Yong Jin
    • , Craig M. Forester
    • , Ying Wang
    • , Craig R. Stumpf
    • , Lingru Xue
    • , Emily Devericks
    • , Lomon So
    • , Hao G. Nguyen
    • , Alice Griselin
    • , John D. Gordan
    • , Saurabh Asthana
    • , John T. Cunningham
    •  & Davide Ruggero
  3. Department of Developmental Biology, Stanford University, Stanford, CA, USA

    • Zhen Shi
    •  & Maria Barna
  4. Department of Genetics, Stanford University, Stanford, CA, USA

    • Zhen Shi
    •  & Maria Barna
  5. Division of Pediatric Allergy, Immunology & Bone Marrow Transplantation, University of California, San Francisco, San Francisco, CA, USA

    • Craig M. Forester
  6. State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China

    • Ying Wang
  7. eFFECTOR Therapeutics, San Diego, CA, USA

    • Craig R. Stumpf
    • , Siegfried H. Reich
    • , Stephen T. Worland
    •  & Kevin R. Webster
  8. Department of Pathology, University of California, San Francisco, CA, USA

    • Sarah E Umetsu
  9. Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA

    • John T. Cunningham
  10. Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA

    • Davide Ruggero

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Contributions

D.R. conceived and supervised the project. Y.X. and M.P. designed and performed most experiments with the help of the other authors. H.Y.J. contributed to the immune profiling analyses, luciferase reporter assays, hydrodynamic tail vein injection and flow cytometry analyses. C.M.F. performed the immune profiling. Y.W., E.D., and A.G. contributed to western blots, cloning, qPCR, CRISPR cell line generation, and intrahepatic HCC graft implantation. J.T.C. developed the MYC transgenic mice and helped C.R.S. with the ribosome profiling and RNA sequencing. L.S. helped with the ribosome-profiling sample preparation. S.A. helped with genome alignment. M.B. and Z.S. performed the bioinformatics analyses related to ribosome profiling and RNA-Seq. H.G.N. and L.X. performed immunofluorescence staining. H.G.N., S.E.U., and J.D.G. provided pathology support and provided human HCC primary samples. K.R.W., S.H.R., and S.T.W. developed and/or supported the development of eFT508. Y.X. and D.R. wrote the manuscript with contributions from M.B., H.Y.J., and C.M.F.

Competing interests

C.R.S., S.H.R. and K.R.W. are employees and shareholders of eFFECTOR Therapeutics, Inc. S.T.W. is the President and CEO of eFFECTOR Therapeutics, Inc. D.R. is a shareholder of eFFECTOR Therapeutics, Inc., and a member of its scientific advisory board.

Corresponding author

Correspondence to Davide Ruggero.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–15

  2. Reporting Summary

  3. Supplementary Table 1

    The transcriptional and translational profiles of gene expression in wild-type (WT) and KRAS-G12D liver tumors

  4. Supplementary Table 2

    The transcriptional and translational profiles of gene expression in KRAS-G12D and MYC-Tg;KRAS-G12D liver tumors

  5. Supplementary Table 3

    Enriched gene ontology categories (biological processes) among 339 transcripts that are translationally induced comparing MYCTg;KRAS-G12D to KRAS-G12D

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https://doi.org/10.1038/s41591-018-0321-2