Abstract
Melanoma tumors are driven by a hyperactivated mitogen-activated protein kinase (MAPK) signalling pathway, and therefore can generally be classified by mutations within the B-Raf proto-oncogene (BRAF), RAS family of proto-oncogenes, neurofibromin 1 (NF1), or other genes. At the transcriptional level, several genetic classifications of melanoma have converged on the distinction between melanogenesis (previously microphthalmia) associated transcription factor (MITF)-low and MITF-high phenotypes and expression of immune-related genes. Mutation-based melanoma subtypes are not prognostic, nor are they associated to transcriptomic subtypes, which are in turn prognostic. Intratumoral heterogeneity of melanoma cells adds another layer of complexity, with recent findings of mutational and transcriptional heterogeneity within melanoma tumors. Furthermore, multiple genetic changes have been associated with different stages of melanoma progression. Mutational signatures may also be differentiated at early and late stages of melanoma progression.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Abbreviations
- cAMP:
-
Cyclic adenosine monophosphate
- CDK:
-
Cyclin-dependent kinase
- COSMIC:
-
Catalogue of Somatic Mutations in Cancer
- CSD:
-
Chronic sun damage
- DNA:
-
Deoxyribonucleic acid
- EMA:
-
European Medicines Agency
- FDA:
-
US Food and Drug Administration
- ITH:
-
Intratumor heterogeneity
- MAPK:
-
Mitogen-activated protein kinase
- TCGA:
-
The Cancer Genome Atlas
- UVB:
-
Ultraviolet B radiation
- UVR:
-
Ultraviolet radiation
References
Cancer Genome Atlas N. Genomic classification of cutaneous melanoma. Cell. 2015;161(7):1681–96. https://doi.org/10.1016/j.cell.2015.05.044.
Cirenajwis H, Lauss M, Ekedahl H, Torngren T, Kvist A, Saal LH, et al. NF1-mutated melanoma tumors harbor distinct clinical and biological characteristics. Mol Oncol. 2017;11(4):438–51. https://doi.org/10.1002/1878-0261.12050.
Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, et al. Mutations of the BRAF gene in human cancer. Nature. 2002;417(6892):949–54. https://doi.org/10.1038/nature00766. nature00766 [pii].
Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, Garraway LA. Highly recurrent TERT promoter mutations in human melanoma. Science. 2013;339(6122):957–9. https://doi.org/10.1126/science.1229259.
Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, Gast A, et al. TERT promoter mutations in familial and sporadic melanoma. Science. 2013;339(6122):959–61. https://doi.org/10.1126/science.1230062.
Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature. 2013;500(7463):415–21. https://doi.org/10.1038/nature12477.
Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, et al. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma. Nat Genet. 2016;48(4):398–406. https://doi.org/10.1038/ng.3525.
Cancer Genome Atlas Research N. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014;159(3):676–90. https://doi.org/10.1016/j.cell.2014.09.050.
Cancer Genome Atlas N. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487(7407):330–7. https://doi.org/10.1038/nature11252.
Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–74. https://doi.org/10.1016/j.cell.2011.02.013.
Shain AH, Bastian BC. From melanocytes to melanomas. Nat Rev Cancer. 2016;16(6):345–58. https://doi.org/10.1038/nrc.2016.37.
Shain AH, Yeh I, Kovalyshyn I, Sriharan A, Talevich E, Gagnon A, et al. The genetic evolution of melanoma from precursor lesions. N Engl J Med. 2015;373(20):1926–36. https://doi.org/10.1056/NEJMoa1502583.
Harbst K, Lauss M, Cirenajwis H, Isaksson K, Rosengren F, Torngren T, et al. Multiregion whole-exome sequencing uncovers the genetic evolution and mutational heterogeneity of early-stage metastatic melanoma. Cancer Res. 2016;76(16):4765–74. https://doi.org/10.1158/0008-5472.CAN-15-3476.
Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000;406(6795):536–40. https://doi.org/10.1038/35020115.
Jonsson G, Busch C, Knappskog S, Geisler J, Miletic H, Ringner M, et al. Gene expression profiling-based identification of molecular subtypes in stage IV melanomas with different clinical outcome. Clin Cancer Res. 2010;16(13):3356–67. https://doi.org/10.1158/1078-0432.CCR-09-2509.
Cirenajwis H, Ekedahl H, Lauss M, Harbst K, Carneiro A, Enoksson J, et al. Molecular stratification of metastatic melanoma using gene expression profiling: prediction of survival outcome and benefit from molecular targeted therapy. Oncotarget. 2015;6(14):12297–309.
Harbst K, Staaf J, Lauss M, Karlsson A, Masback A, Johansson I, et al. Molecular profiling reveals low- and high-grade forms of primary melanoma. Clin Cancer Res. 2012;18(15):4026–36. https://doi.org/10.1158/1078-0432.CCR-12-0343.
Lauss M, Nsengimana J, Staaf J, Newton-Bishop J, Jonsson G. Consensus of melanoma gene expression subtypes converges on biological entities. J Invest Dermatol. 2016;136(12):2502–5. https://doi.org/10.1016/j.jid.2016.05.119.
Bertolotto C, Lesueur F, Giuliano S, Strub T, de Lichy M, Bille K, et al. A SUMOylation-defective MITF germline mutation predisposes to melanoma and renal carcinoma. Nature. 2011;480(7375):94–8. https://doi.org/10.1038/nature10539.
Yokoyama S, Woods SL, Boyle GM, Aoude LG, MacGregor S, Zismann V, et al. A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma. Nature. 2011;480(7375):99–103. https://doi.org/10.1038/nature10630.
Wellbrock C, Arozarena I. Microphthalmia-associated transcription factor in melanoma development and MAP-kinase pathway targeted therapy. Pigment Cell Melanoma Res. 2015;28(4):390–406. https://doi.org/10.1111/pcmr.12370.
Hoek KS, Schlegel NC, Brafford P, Sucker A, Ugurel S, Kumar R, et al. Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature. Pigment Cell Res. 2006;19(4):290–302. https://doi.org/10.1111/j.1600-0749.2006.00322.x.
Widmer DS, Cheng PF, Eichhoff OM, Belloni BC, Zipser MC, Schlegel NC, et al. Systematic classification of melanoma cells by phenotype-specific gene expression mapping. Pigment Cell Melanoma Res. 2012;25(3):343–53. https://doi.org/10.1111/j.1755-148X.2012.00986.x.
Howlin J, Cirenajwis H, Lettiero B, Staaf J, Lauss M, Saal L, et al. Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours. Peer J. 2015;3:e788. https://doi.org/10.7717/peerj.788.
Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352(6282):189–96. https://doi.org/10.1126/science.aad0501.
Mandruzzato S, Callegaro A, Turcatel G, Francescato S, Montesco MC, Chiarion-Sileni V, et al. A gene expression signature associated with survival in metastatic melanoma. J Transl Med. 2006;4:50. https://doi.org/10.1186/1479-5876-4-50.
Bogunovic D, O'Neill DW, Belitskaya-Levy I, Vacic V, Yu YL, Adams S, et al. Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival. Proc Natl Acad Sci U S A. 2009;106(48):20429–34. https://doi.org/10.1073/pnas.0905139106.
Mann GJ, Pupo GM, Campain AE, Carter CD, Schramm SJ, Pianova S, et al. BRAF mutation, NRAS mutation, and the absence of an immune-related expressed gene profile predict poor outcome in patients with stage III melanoma. J Invest Dermatol. 2013;133(2):509–17. https://doi.org/10.1038/jid.2012.283.
Maio M. Melanoma as a model tumour for immuno-oncology. Ann Oncol. 2012;23(Suppl 8):viii10–viii4. https://doi.org/10.1093/annonc/mds257.
Wenzel J, Bekisch B, Uerlich M, Haller O, Bieber T, Tuting T. Type I interferon-associated recruitment of cytotoxic lymphocytes: a common mechanism in regressive melanocytic lesions. Am J Clin Pathol. 2005;124(1):37–48. https://doi.org/10.1309/4EJ9KL7CGDENVVLE.
Redondo P, Del Olmo J. Images in clinical medicine. Vitiligo and cutaneous melanoma. N Engl J Med. 2008;359(3):e3. https://doi.org/10.1056/NEJMicm053764.
Nordlund JJ, Kirkwood JM, Forget BM, Milton G, Albert DM, Lerner AB. Vitiligo in patients with metastatic melanoma: a good prognostic sign. J Am Acad Dermatol. 1983;9(5):689–96.
Kitamura T, Qian BZ, Pollard JW. Immune cell promotion of metastasis. Nat Rev Immunol. 2015;15(2):73–86. https://doi.org/10.1038/nri3789.
Thor Straten P, Garrido F. Targetless T cells in cancer immunotherapy. J Immunother Cancer. 2016;4:23. https://doi.org/10.1186/s40425-016-0127-z.
Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol. 2015;33:1152–8. https://doi.org/10.1038/nbt.3344.
Teulings HE, Limpens J, Jansen SN, Zwinderman AH, Reitsma JB, Spuls PI, et al. Vitiligo-like depigmentation in patients with stage III–IV melanoma receiving immunotherapy and its association with survival: a systematic review and meta-analysis. J Clin Oncol. 2015;33(7):773–81. https://doi.org/10.1200/JCO.2014.57.4756.
Riker AI, Enkemann SA, Fodstad O, Liu S, Ren S, Morris C, et al. The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis. BMC Med Genet. 2008;1:13. https://doi.org/10.1186/1755-8794-1-13.
Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 2012;366(10):883–92. https://doi.org/10.1056/NEJMoa1113205.
Gerlinger M, Horswell S, Larkin J, Rowan AJ, Salm MP, Varela I, et al. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet. 2014;46(3):225–33. https://doi.org/10.1038/ng.2891.
Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet. 2015;47(7):736–45. https://doi.org/10.1038/ng.3315.
Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, et al. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet. 2015;47(4):367–72. https://doi.org/10.1038/ng.3221.
Murugaesu N, Wilson GA, Birkbak NJ, Watkins TB, McGranahan N, Kumar S, et al. Tracking the genomic evolution of esophageal adenocarcinoma through neoadjuvant chemotherapy. Cancer Discov. 2015;5(8):821–31. https://doi.org/10.1158/2159-8290.CD-15-0412.
Bashashati A, Ha G, Tone A, Ding J, Prentice LM, Roth A, et al. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling. J Pathol. 2013;231(1):21–34. https://doi.org/10.1002/path.4230.
Zhang J, Fujimoto J, Zhang J, Wedge DC, Song X, Zhang J, et al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science. 2014;346(6206):256–9. https://doi.org/10.1126/science.1256930.
de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science. 2014;346(6206):251–6. https://doi.org/10.1126/science.1253462.
Jamal-Hanjani M, Wilson GA, McGranahan N, Birkbak NJ, Watkins TBK, Veeriah S, et al. Tracking the evolution of non-small-cell lung cancer. N Engl J Med. 2017;376(22):2109–21. https://doi.org/10.1056/NEJMoa1616288.
Morris LG, Riaz N, Desrichard A, Senbabaoglu Y, Hakimi AA, Makarov V, et al. Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival. Oncotarget. 2016;7(9):10051–63. https://doi.org/10.18632/oncotarget.7067.
Li Q, Wennborg A, Aurell E, Dekel E, Zou JZ, Xu Y, et al. Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape. Proc Natl Acad Sci U S A. 2016;113(10):2672–7. https://doi.org/10.1073/pnas.1519210113.
Eichhoff OM, Weeraratna A, Zipser MC, Denat L, Widmer DS, Xu M, et al. Differential LEF1 and TCF4 expression is involved in melanoma cell phenotype switching. Pigment Cell Melanoma Res. 2011;24(4):631–42. https://doi.org/10.1111/1755-148X.2011.00871.x.
Hoek KS, Eichhoff OM, Schlegel NC, Dobbeling U, Kobert N, Schaerer L, et al. In vivo switching of human melanoma cells between proliferative and invasive states. Cancer Res. 2008;68(3):650–6. https://doi.org/10.1158/0008-5472.CAN-07-2491.
Cleary AS, Leonard TL, Gestl SA, Gunther EJ. Tumour cell heterogeneity maintained by cooperating subclones in Wnt-driven mammary cancers. Nature. 2014;508(7494):113–7. https://doi.org/10.1038/nature13187.
Muller J, Krijgsman O, Tsoi J, Robert L, Hugo W, Song C, et al. Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma. Nat Commun. 2014;5:5712. https://doi.org/10.1038/ncomms6712.
Konieczkowski DJ, Johannessen CM, Abudayyeh O, Kim JW, Cooper ZA, Piris A, et al. A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Cancer Discov. 2014;4(7):816–27. https://doi.org/10.1158/2159-8290.CD-13-0424.
Harbst K, Lauss M, Cirenajwis H, Winter C, Howlin J, Torngren T, et al. Molecular and genetic diversity in the metastatic process of melanoma. J Pathol. 2014;233(1):39–50. https://doi.org/10.1002/path.4318.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Harbst, K., Jönsson, G. (2018). The Genetic Evolution of Melanoma. In: Riker, A. (eds) Melanoma. Springer, Cham. https://doi.org/10.1007/978-3-319-78310-9_6
Download citation
DOI: https://doi.org/10.1007/978-3-319-78310-9_6
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-78309-3
Online ISBN: 978-3-319-78310-9
eBook Packages: MedicineMedicine (R0)