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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

References

  1. 1.

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

  2. 2.

    , , , & Desmoplastic melanoma: a review. J. Am. Acad. Dermatol. 68, 825–833 (2013).

  3. 3.

    , & Desmoplastic melanoma—the step-child in the melanoma family? J. Surg. Oncol. 103, 158–162 (2011).

  4. 4.

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

  5. 5.

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

  6. 6.

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

  7. 7.

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

  8. 8.

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

  9. 9.

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

  10. 10.

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

  11. 11.

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

  12. 12.

    & Raising the bar for melanoma cancer gene discovery. Pigment Cell Melanoma Res. 25, 708–709 (2012).

  13. 13.

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

  14. 14.

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

  15. 15.

    & Negative regulation of PTK signalling by Cbl proteins. Growth Factors 23, 161–167 (2005).

  16. 16.

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

  17. 17.

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

  18. 18.

    , , , & 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).

  19. 19.

    , & MEKK1 binds raf-1 and the ERK2 cascade components. J. Biol. Chem. 275, 40120–40127 (2000).

  20. 20.

    , , , & Low-copy piggyBac transposon mutagenesis in mice identifies genes driving melanoma. Proc. Natl. Acad. Sci. USA 110, E3640–E3649 (2013).

  21. 21.

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

  22. 22.

    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).

  23. 23.

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

  24. 24.

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

  25. 25.

    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).

  26. 26.

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

  27. 27.

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

  28. 28.

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

  29. 29.

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

  30. 30.

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

  31. 31.

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

  32. 32.

    , & 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).

  33. 33.

    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).

  34. 34.

    , , & Activation of nuclear factor–κB in human metastatic melanomacells and the effect of oxidative stress. Clin. Cancer Res. 5, 1197–1202 (1999).

  35. 35.

    , , , & Wild-type and mutant B-RAF activate C-RAF through distinct mechanisms involving heterodimerization. Mol. Cell 20, 963–969 (2005).

  36. 36.

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

  37. 37.

    & The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PLoS ONE 8, e55119 (2013).

  38. 38.

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

  39. 39.

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

  40. 40.

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

  41. 41.

    , & CNVkit: copy number detection and visualization for targeted sequencing using off-target reads. bioRxiv 10.1101/010876 (2014).

  42. 42.

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

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

Author notes

    • Raymond J Cho
    • , Rajmohan Murali
    •  & Boris C Bastian

    These authors contributed equally to this work.

Affiliations

  1. Department of Pathology, University of California, San Francisco, San Francisco, California, USA.

    • A Hunter Shain
    • , Maria Garrido
    • , Thomas Botton
    • , Eric Talevich
    • , Iwei Yeh
    • , Alexander Gagnon
    •  & Boris C Bastian
  2. Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA.

    • A Hunter Shain
    • , Maria Garrido
    • , Thomas Botton
    • , Eric Talevich
    • , Iwei Yeh
    • , Ritu Roy
    • , Adam B Olshen
    • , Alexander Gagnon
    •  & Boris C Bastian
  3. Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.

    • A Hunter Shain
    • , Maria Garrido
    • , Thomas Botton
    • , Eric Talevich
    • , Iwei Yeh
    • , Alexander Gagnon
    • , Raymond J Cho
    •  & Boris C Bastian
  4. Five3 Genomics, LLC, Santa Cruz, California, USA.

    • J Zachary Sanborn
  5. Samsung Advanced Institute of Technology, Seoul, Korea.

    • Jongsuk Chung
    •  & Nam Huh
  6. Department of Biomedical Engineering, Oregon Health and Sciences University, Portland, Oregon, USA.

    • Nicholas J Wang
    •  & Joe W Gray
  7. Knight Cancer Institute, Oregon Health and Sciences University, Portland, Oregon, USA.

    • Nicholas J Wang
    •  & Joe W Gray
  8. Melanoma Institute Australia, Sydney, New South Wales, Australia.

    • Hojabr Kakavand
    • , Graham J Mann
    • , John F Thompson
    •  & Richard A Scolyer
  9. Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.

    • Hojabr Kakavand
    • , Graham J Mann
    • , John F Thompson
    •  & Richard A Scolyer
  10. Royal Prince Alfred Hospital, Sydney, New South Wales, Australia.

    • John F Thompson
    •  & Richard A Scolyer
  11. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Thomas Wiesner
  12. Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.

    • Adam B Olshen
  13. Samsung Electronics Headquarters, Seoul, Korea.

    • Joe S Hur
  14. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Klaus J Busam
    •  & Rajmohan Murali
  15. Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Rajmohan Murali

Authors

  1. Search for A Hunter Shain in:

  2. Search for Maria Garrido in:

  3. Search for Thomas Botton in:

  4. Search for Eric Talevich in:

  5. Search for Iwei Yeh in:

  6. Search for J Zachary Sanborn in:

  7. Search for Jongsuk Chung in:

  8. Search for Nicholas J Wang in:

  9. Search for Hojabr Kakavand in:

  10. Search for Graham J Mann in:

  11. Search for John F Thompson in:

  12. Search for Thomas Wiesner in:

  13. Search for Ritu Roy in:

  14. Search for Adam B Olshen in:

  15. Search for Alexander Gagnon in:

  16. Search for Joe W Gray in:

  17. Search for Nam Huh in:

  18. Search for Joe S Hur in:

  19. Search for Klaus J Busam in:

  20. Search for Richard A Scolyer in:

  21. Search for Raymond J Cho in:

  22. Search for Rajmohan Murali in:

  23. Search for Boris C Bastian in:

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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Boris C Bastian.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11.

Excel files

  1. 1.

    Supplementary Table 1: Sample descriptions.

  2. 2.

    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.

  3. 3.

    Supplementary Table 3: Discovery mutations.

  4. 4.

    Supplementary Table 4: Validation mutations.

  5. 5.

    Supplementary Table 5: NFKBIE mutation details.

  6. 6.

    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.

About this article

Publication history

Received

Accepted

Published

DOI

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

Further reading

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