Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway

Abstract

Desmoplastic melanoma is an uncommon variant of melanoma with sarcomatous histology, distinct clinical behavior and unknown pathogenesis1,2,3. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes in a validation cohort of 42 cases. A high mutation burden (median of 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers4. Mutation patterns strongly implicate ultraviolet radiation as the dominant mutagen5, indicating a superficially located cell of origin. Newly identified alterations included recurrent promoter mutations of NFKBIE, encoding NF-κB inhibitor ɛ (IκBɛ), in 14.5% of samples. Common oncogenic mutations in melanomas, in particular in BRAF (encoding p.Val600Glu) and NRAS (encoding p.Gln61Lys or p.Gln61Arg), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS and PIK3CA, some of which are candidates for targeted therapies.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Desmoplastic melanomas have a substantial point mutation burden consistent with UV radiation–induced damage.
Figure 2: Nomination of driver mutations in desmoplastic melanoma.
Figure 3: Genetic alterations of CBL, MAP3K1, FBXW7 and NFKBIE.
Figure 4: Recurrent mutations affect the promoter of NFKBIE.
Figure 5: The mutational landscape of desmoplastic melanoma.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

References

  1. Quinn, M.J. et al. Desmoplastic and desmoplastic neurotropic melanoma: experience with 280 patients. Cancer 83, 1128–1135 (1998).

    Article  CAS  Google Scholar 

  2. Chen, L.L., Jaimes, N., Barker, C.A., Busam, K.J. & Marghoob, A.A. Desmoplastic melanoma: a review. J. Am. Acad. Dermatol. 68, 825–833 (2013).

    Article  Google Scholar 

  3. Wasif, N., Gray, R.J. & Pockaj, B.A. Desmoplastic melanoma—the step-child in the melanoma family? J. Surg. Oncol. 103, 158–162 (2011).

    Article  Google Scholar 

  4. Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546–1558 (2013).

    Article  CAS  Google Scholar 

  5. Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).

    Article  CAS  Google Scholar 

  6. Murali, R. et al. Prognostic factors in cutaneous desmoplastic melanoma: a study of 252 patients. Cancer 116, 4130–4138 (2010).

    Article  Google Scholar 

  7. Busam, K.J. et al. Cutaneous desmoplastic melanoma: reappraisal of morphologic heterogeneity and prognostic factors. Am. J. Surg. Pathol. 28, 1518–1525 (2004).

    Article  Google Scholar 

  8. Davison, J.M. et al. Absence of V599E BRAF mutations in desmoplastic melanomas. Cancer 103, 788–792 (2005).

    Article  CAS  Google Scholar 

  9. Kim, J. et al. BRAF, NRAS and KIT sequencing analysis of spindle cell melanoma. J. Cutan. Pathol. 39, 821–825 (2012).

    Article  Google Scholar 

  10. Hodis, E. et al. A landscape of driver mutations in melanoma. Cell 150, 251–263 (2012).

    Article  CAS  Google Scholar 

  11. Krauthammer, M. et al. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat. Genet. 44, 1006–1014 (2012).

    Article  CAS  Google Scholar 

  12. Shain, A.H. & Bastian, B.C. Raising the bar for melanoma cancer gene discovery. Pigment Cell Melanoma Res. 25, 708–709 (2012).

    Article  Google Scholar 

  13. Horn, S. et al. TERT promoter mutations in familial and sporadic melanoma. Science 339, 959–961 (2013).

    Article  CAS  Google Scholar 

  14. Huang, F.W. et al. Highly recurrent TERT promoter mutations in human melanoma. Science 339, 957–959 (2013).

    Article  CAS  Google Scholar 

  15. Thien, C.B.F. & Langdon, W.Y. Negative regulation of PTK signalling by Cbl proteins. Growth Factors 23, 161–167 (2005).

    Article  CAS  Google Scholar 

  16. Niemeyer, C.M. et al. Germline CBL mutations cause developmental abnormalities and predispose to juvenile myelomonocytic leukemia. Nat. Genet. 42, 794–800 (2010).

    Article  CAS  Google Scholar 

  17. Bastian, B.C. The molecular pathology of melanoma: an integrated taxonomy of melanocytic neoplasia. Annu. Rev. Pathol. 9, 239–271 (2014).

    Article  CAS  Google Scholar 

  18. Blank, J.L., Gerwins, P., Elliott, E.M., Sather, S. & Johnson, G.L. Molecular cloning of mitogen-activated protein/ERK kinase kinases (MEKK) 2 and 3. Regulation of sequential phosphorylation pathways involving mitogen-activated protein kinase and c-Jun kinase. J. Biol. Chem. 271, 5361–5368 (1996).

    Article  CAS  Google Scholar 

  19. Karandikar, M., Xu, S. & Cobb, M.H. MEKK1 binds raf-1 and the ERK2 cascade components. J. Biol. Chem. 275, 40120–40127 (2000).

    Article  CAS  Google Scholar 

  20. Ni, T.K., Landrette, S.F., Bjornson, R.D., Bosenberg, M.W. & Xu, T. Low-copy piggyBac transposon mutagenesis in mice identifies genes driving melanoma. Proc. Natl. Acad. Sci. USA 110, E3640–E3649 (2013).

    Article  CAS  Google Scholar 

  21. Koepp, D.M. et al. Phosphorylation-dependent ubiquitination of cyclin E by the SCFFbw7 ubiquitin ligase. Science 294, 173–177 (2001).

    Article  CAS  Google Scholar 

  22. Welcker, M. et al. The Fbw7 tumor suppressor regulates glycogen synthase kinase 3 phosphorylation-dependent c-Myc protein degradation. Proc. Natl. Acad. Sci. USA 101, 9085–9090 (2004).

    Article  CAS  Google Scholar 

  23. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).

  24. Ojesina, A.I. et al. Landscape of genomic alterations in cervical carcinomas. Nature 506, 371–375 (2014).

    Article  CAS  Google Scholar 

  25. Shern, J.F. et al. Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. Cancer Discov. 4, 216–231 (2014).

    Article  CAS  Google Scholar 

  26. Wei, X. et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat. Genet. 43, 442–446 (2011).

    Article  CAS  Google Scholar 

  27. Nikolaev, S.I. et al. Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat. Genet. 44, 133–139 (2012).

    Article  CAS  Google Scholar 

  28. Stark, M.S. et al. Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing. Nat. Genet. 44, 165–169 (2012).

    Article  CAS  Google Scholar 

  29. Aydin, I.T. et al. FBXW7 mutations in melanoma and a new therapeutic paradigm. J. Natl. Cancer Inst. 106, dju107 (2014).

    Article  Google Scholar 

  30. Hayden, M.S. & Ghosh, S. NF-κB, the first quarter-century: remarkable progress and outstanding questions. Genes Dev. 26, 203–234 (2012).

    Article  CAS  Google Scholar 

  31. Yang, J. & Richmond, A. Constitutive IκB kinase activity correlates with nuclear factor–κB activation in human melanoma cells. Cancer Res. 61, 4901–4909 (2001).

    CAS  PubMed  Google Scholar 

  32. McNulty, S.E., Tohidian, N.B. & Meyskens, F.L. RelA, p50 and inhibitor of kappa B alpha are elevated in human metastatic melanoma cells and respond aberrantly to ultraviolet light B. Pigment Cell Res. 14, 456–465 (2001).

    Article  CAS  Google Scholar 

  33. Franco, A.V. et al. The role of NF-κB in TNF-related apoptosis-inducing ligand (TRAIL)-induced apoptosis of melanoma cells. J. Immunol. 166, 5337–5345 (2001).

    Article  CAS  Google Scholar 

  34. Meyskens, F.L., Buckmeier, J.A., McNulty, S.E. & Tohidian, N.B. Activation of nuclear factor–κB in human metastatic melanomacells and the effect of oxidative stress. Clin. Cancer Res. 5, 1197–1202 (1999).

    CAS  PubMed  Google Scholar 

  35. Garnett, M.J., Rana, S., Paterson, H., Barford, D. & Marais, R. Wild-type and mutant B-RAF activate C-RAF through distinct mechanisms involving heterodimerization. Mol. Cell 20, 963–969 (2005).

    Article  CAS  Google Scholar 

  36. Heidorn, S.J. et al. Kinase-dead BRAF and oncogenic RAS cooperate to drive tumor progression through CRAF. Cell 140, 209–221 (2010).

    Article  CAS  Google Scholar 

  37. Shain, A.H. & Pollack, J.R. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PLoS ONE 8, e55119 (2013).

    Article  Google Scholar 

  38. Snyder, A. et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N. Engl. J. Med. 371, 2189–2199 (2014).

    Article  Google Scholar 

  39. Venkatraman, E.S. & Olshen, A.B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657–663 (2007).

    Article  CAS  Google Scholar 

  40. Curtin, J.A. et al. Distinct sets of genetic alterations in melanoma. N. Engl. J. Med. 353, 2135–2147 (2005).

    Article  CAS  Google Scholar 

  41. Talevich, E., Shain, A.H. & Bastian, B.C. CNVkit: copy number detection and visualization for targeted sequencing using off-target reads. bioRxiv 10.1101/010876 (2014).

  42. Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2, 82–93 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by US National Institutes of Health grants R01 CA131524 (B.C.B.), P01 CA025874 (B.C.B.), P30 CA82103 (A.B.O.) and 5T32 CA177555-02 (A.H.S.), the American Skin Association (B.C.B.), the Gerson and Barbara Bakar Distinguished Chair in Cancer Biology (B.C.B.), the Well Aging Research Center at the Samsung Advanced Institute of Technology under the auspices of S.C. Park, the Dermatology Foundation and US National Institutes of Health grants K08 CA169865 (R.J.C.), U54 CA112970 (J.W.G.) and the Oregon Health and Sciences University Knight Cancer Institute 5P30 CA069533 (J.W.G.). The authors acknowledge support from the Australian National Health and Medical Research Council, Cancer Institute New South Wales, the Melanoma Foundation of the University of Sydney and the staff of Melanoma Institute Australia and Royal Prince Alfred Hospital. Finally, we would like to thank A. Ribas (UCLA Jonsson Comprehensive Cancer Center) and G. Long (Melanoma Institute Australia) for providing samples used in this study.

Author information

Authors and Affiliations

Authors

Contributions

A.H.S., R.M. and B.C.B. designed the study. M.G., I.Y., H.K., G.J.M., J.F.T., T.W., K.J.B., R.A.S., R.M. and B.C.B. provided cases. A.H.S., M.G., I.Y., K.J.B., R.A.S., R.M. and B.C.B. evaluated and/or microdissected cases. J.C., N.J.W., A.G., J.W.G., N.H., J.S.H., R.J.C. and B.C.B. sequenced samples. A.H.S., M.G., R.R., A.B.O., E.T. and B.C.B. analyzed copy number data. A.H.S., J.Z.S., R.J.C. and B.C.B. analyzed sequencing data. A.H.S. and R.M. carried out immunohistochemistry. A.H.S. and T.B. performed Sanger sequencing, RT-PCR, immunoblots and cell culture work. A.H.S. and B.C.B. wrote the manuscript. All authors reviewed the manuscript.

Corresponding author

Correspondence to Boris C Bastian.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11. (PDF 10459 kb)

Supplementary Table 1: Sample descriptions. (XLSX 35 kb)

Supplementary Table 2: Target intervals.

The 293 genes included in the validation cohort are listed in tab 1. The second tab describes the actual genomic intervals tiled. (XLSX 400 kb)

Supplementary Table 3: Discovery mutations. (XLSX 2685 kb)

Supplementary Table 4: Validation mutations. (XLSX 388 kb)

Supplementary Table 5: NFKBIE mutation details. (XLSX 50 kb)

Supplementary Table 6: Copy number circular binary segmentation (CBS) calls.

CBS calls generated from the higher-resolution primary copy number platform (Supplementary Table 1) are listed in the first tab. For many samples, copy number was also inferred using an orthogonal assay, and those copy number calls are listed in the second tab. Copy number data agreed very well between the two platforms. (XLSX 1141 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shain, A., Garrido, M., Botton, T. et al. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nat Genet 47, 1194–1199 (2015). https://doi.org/10.1038/ng.3382

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3382

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing