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Abstract

Treatment of BRAF(V600E) mutant melanoma by small molecule drugs that target the BRAF or MEK kinases can be effective, but resistance develops invariably1,2. In contrast, colon cancers that harbour the same BRAF(V600E) mutation are intrinsically resistant to BRAF inhibitors, due to feedback activation of the epidermal growth factor receptor (EGFR)3,4. Here we show that 6 out of 16 melanoma tumours analysed acquired EGFR expression after the development of resistance to BRAF or MEK inhibitors. Using a chromatin-regulator-focused short hairpin RNA (shRNA) library, we find that suppression of sex determining region Y-box 10 (SOX10) in melanoma causes activation of TGF-β signalling, thus leading to upregulation of EGFR and platelet-derived growth factor receptor-β (PDGFRB), which confer resistance to BRAF and MEK inhibitors. Expression of EGFR in melanoma or treatment with TGF-β results in a slow-growth phenotype with cells displaying hallmarks of oncogene-induced senescence. However, EGFR expression or exposure to TGF-β becomes beneficial for proliferation in the presence of BRAF or MEK inhibitors. In a heterogeneous population of melanoma cells having varying levels of SOX10 suppression, cells with low SOX10 and consequently high EGFR expression are rapidly enriched in the presence of drug, but this is reversed when the drug treatment is discontinued. We find evidence for SOX10 loss and/or activation of TGF-β signalling in 4 of the 6 EGFR-positive drug-resistant melanoma patient samples. Our findings provide a rationale for why some BRAF or MEK inhibitor-resistant melanoma patients may regain sensitivity to these drugs after a ‘drug holiday’ and identify patients with EGFR-positive melanoma as a group that may benefit from re-treatment after a drug holiday.

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Primary accessions

Gene Expression Omnibus

Data deposits

RNA sequencing data are available at Gene Expression Omnibus with accession code GSE50535.

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Acknowledgements

We thank the NKI Core Facilities for Genomics and Molecular Pathology & Biobanking for tumour tissue and support in DNA sequencing. We thank S. Roy for collecting clinical data and N. Kamsu Kom for tissue preparation. This work was supported by grants from the European Research Council (ERC), the Dutch Cancer Society (KWF), the EU COLTHERES project and grants by the Netherlands Organization for Scientific Research (NWO) to Cancer Genomics Netherlands (CGC.NL). Additional support was provided by Fondazione Piemontese per la Ricerca sul Cancro—ONLUS grant ‘Farmacogenomica—5 per mille 2009 MIUR’ (F.D.N.); AIRC MFAG 11349 (F.D.N.); AIRC IG grant n. 12812 (A.B.); and Canadian Institutes of Health Research (CIHR) grant MOP-130540 (S.Hu).

Author information

Author notes

    • Chong Sun
    • , Liqin Wang
    •  & Sidong Huang

    These authors contributed equally to this work.

Affiliations

  1. Division of Molecular Carcinogenesis, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Chong Sun
    • , Liqin Wang
    • , Sidong Huang
    • , Guus J. J. E. Heynen
    • , Anirudh Prahallad
    • , Stefan M. Willems
    • , Prashanth K. Bajpe
    • , Cor Lieftink
    • , Wipawadee Grernrum
    • , Andreas Schlicker
    • , Lodewyk F. A. Wessels
    • , Roderick L. Beijersbergen
    •  & Rene Bernards
  2. Department of Biochemistry, The Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec H3G 1Y6, Canada

    • Sidong Huang
  3. Institut Gustave Roussy, 114 Rue Edouard Vaillant, 94800 Villejuif, France

    • Caroline Robert
    • , Christina Mateus
    • , Stephan Vagner
    •  & Alexander M. M. Eggermont
  4. Division of Medical Oncology, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • John Haanen
    •  & Christian Blank
  5. Division of Pathology, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

    • Jelle Wesseling
    •  & Ingrid Hofland
  6. Department of Pathology, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands

    • Stefan M. Willems
  7. University of Torino, Department of Oncology, Str prov 142 Km 3.95, 10060 Candiolo, Torino, Italy

    • Davide Zecchin
    • , Alberto Bardelli
    •  & Federica Di Nicolantonio
  8. Candiolo Cancer Institute – FPO, IRCCS, Str prov 142 Km 3.95, 10060 Candiolo, Torino, Italy

    • Davide Zecchin
    • , Sebastijan Hobor
    • , Alberto Bardelli
    •  & Federica Di Nicolantonio
  9. FIRC Institute of Molecular Oncology (IFOM), 20139 Milano, Italy

    • Alberto Bardelli

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Contributions

R.B., A.B., F.D.N., L.F.A.W., C.R., R.L.B. and A.M.M.E. supervised all research. R.B. and C.S. wrote the manuscript. C.S., L.W., S.Hu., G.J.J.E.H., A.P., D.Z., S.Ho., P.K.B., C.L., C.M., S.V., J.W., W.G., I.H. and A.S. designed and performed experiments and J.H., C.B., C.R., S.M.W., S.V. and A.M.M.E. provided clinical samples and gave advice.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Rene Bernards.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    This table contains patient information.

  2. 2.

    Supplementary Table 2

    A list of genes in chromatin library.

  3. 3.

    Supplementary Table 3

    Top hits from genetic screen.

  4. 4.

    Supplementary Table 4

    RNAseq data from shSOX10 cells.

  5. 5.

    Supplementary Table 5

    Gene Set Enrichment Analysis of SOX10 regulated genes.

  6. 6.

    Supplementary Table 6

    shRNA IDs and sequences.

  7. 7.

    Supplementary Table 7

    List of QRT-PCR primers used.

About this article

Publication history

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DOI

https://doi.org/10.1038/nature13121

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