Abstract

The clinical benefit for patients with diverse types of metastatic cancers that has been observed upon blockade of the interaction between PD-1 and PD-L1 has highlighted the importance of this inhibitory axis in the suppression of tumour-specific T-cell responses1,2,3,4,5,6,7,8,9. Notwithstanding the key role of PD-L1 expression by cells within the tumour micro-environment, our understanding of the regulation of the PD-L1 protein is limited10,11,12,13,14,15. Here we identify, using a haploid genetic screen, CMTM6, a type-3 transmembrane protein of previously unknown function, as a regulator of the PD-L1 protein. Interference with CMTM6 expression results in impaired PD-L1 protein expression in all human tumour cell types tested and in primary human dendritic cells. Furthermore, through both a haploid genetic modifier screen in CMTM6-deficient cells and genetic complementation experiments, we demonstrate that this function is shared by its closest family member, CMTM4, but not by any of the other CMTM members tested. Notably, CMTM6 increases the PD-L1 protein pool without affecting PD-L1 (also known as CD274) transcription levels. Rather, we demonstrate that CMTM6 is present at the cell surface, associates with the PD-L1 protein, reduces its ubiquitination and increases PD-L1 protein half-life. Consistent with its role in PD-L1 protein regulation, CMTM6 enhances the ability of PD-L1-expressing tumour cells to inhibit T cells. Collectively, our data reveal that PD-L1 relies on CMTM6/4 to efficiently carry out its inhibitory function, and suggest potential new avenues to block this pathway.

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Acknowledgements

We thank F. Scheeren, E. Stickel, V. Blomen, M. Brockmann and the other members of the Schumacher and Brummelkamp laboratories for discussions, J. Grabowska for technical assistance, K. Kemper and D. Peeper for sharing melanoma PDX models and the NKI- AVL flow facility, the NKI-AVL Core Facility Molecular Pathology & Biobanking (CFMPB) for supplying NKI-AVL Biobank material and/or laboratory support. This work was supported by The Queen Wilhelmina Cancer Research Award and European Research Council (ERC) Advanced Grant SENSIT (to T.N.M.S.), NWO Vici Grant (016.Vici.170.033), the Cancer Genomics Center (CGC.nl), and Ammodo KNAW Award 2015 for Biomedical Sciences (to T.R.B.), The Cancer Research Institute (CRI) Irvington Postdoctoral Fellowship (to C.S.), The Landsteiner Foundation for Blood Research, grant 1355 (to J.B.), Proteins@Work, a program of the Netherlands Proteomics Centre financed by NWO, the Netherlands Organisation for Scientific Research (to A.J.R.H.) and The Institute for Chemical Immunology, an NWO Gravitation project (to T.N.M.S. and A.J.R.H.).

Author information

Author notes

    • Riccardo Mezzadra
    • , Chong Sun
    •  & Lucas T. Jae

    These authors contributed equally to this work.

    • Lucas T. Jae

    Present address: Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.

Affiliations

  1. Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Riccardo Mezzadra
    • , Chong Sun
    • , Raquel Gomez-Eerland
    • , Meike E. W. Logtenberg
    • , Maarten Slagter
    • , Elisa A. Rozeman
    • , Christian U. Blank
    •  & Ton N. M. Schumacher
  2. Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Lucas T. Jae
    •  & Thijn R. Brummelkamp
  3. Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Evert de Vries
    • , Yanling Xiao
    •  & Jannie Borst
  4. Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, The Netherlands

    • Wei Wu
    •  & Albert J. R. Heck
  5. Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands

    • Wei Wu
    •  & Albert J. R. Heck
  6. Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Maarten Slagter
    •  & Lodewyk F. A. Wessels
  7. Division of Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Elisa A. Rozeman
    •  & Christian U. Blank
  8. Core Facility Molecular Pathology & Biobanking, Division of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Ingrid Hofland
    •  & Annegien Broeks
  9. Division of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Hugo M. Horlings
  10. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria

    • Thijn R. Brummelkamp
  11. Cancergenomics.nl, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Thijn R. Brummelkamp

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Contributions

R.M., C.S. and L.T.J. conceived the project, designed and performed experiments, interpreted data and co-wrote the paper. R.G.-E. designed, performed and interpreted functional assays. W.W. designed, performed and interpreted mass spectrometry analyses, A.J.R.H. designed and interpreted mass spectrometry analyses, E.d.V. designed, performed and interpreted immunoprecipitation experiments, Y.X. designed, performed and interpreted human dendritic cell experiments, M.E.W.L. performed and interpreted melanoma PDX experiments, M.S. performed bioinformatic analyses, L.F.A.W. supervised bioinformatic analysis, E.A.R. and I.H. identified samples and performed immunohistochemistry analyses, A.B. and H.M.H. supervised and scored immunohistochemistry analyses, C.U.B. provided and identified samples for immunohistochemistry analyses, J.B. designed and interpreted immunoprecipitation and human dendritic cell experiments, T.R.B. and T.N.M.S. designed experiments, interpreted data and co-wrote the manuscript.

Competing interests

R.M., C.S., L.T.J., T.R.B. and T.N.M.S. are inventors on a patent application covering the use of CMTM6, CMTM4 and STUB1 as therapeutic and diagnostic targets. T.R.B. is co-founder and shareholder of Scenic Biotech. The other authors declare no competing interests

Corresponding authors

Correspondence to Thijn R. Brummelkamp or Ton N. M. Schumacher.

Reviewer Information Nature thanks S. Ogawa, A. Ribas 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.

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