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Epigenetics in Melanoma

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Abstract

Melanoma is a highly heterogeneous malignancy that is the result of the accumulation of genetic and epigenetic defects. Genome and transcriptome analyses and extensive studies in DNA methylation, chromatin modifications and nucleosome positioning have revolutionised our genetic and epigenetic knowledge of melanoma over the last decade. Recent progress in melanoma research has shown that epigenetic events play key roles in establishing the correct programme of gene expression. In particular, epigenetics research is unveiling new perspectives on the biology of melanoma and identifying new strategies to fight this disease. DNA methylation and chromatin-modifying enzymes can be used as putative targets for better therapy. On the other hand non-coding RNAs such as miRNAs and snoRNAs are likely being used as diagnostic or prognostic biomarkers for melanoma patients. Long non-coding RNAs function as regulatory molecules in several pathways in melanoma. Deregulation of various long non-coding RNAs in melanoma has been reported. Long non-coding RNAs can be targeted by antisense oligonucleotide or small molecules in order to inhibit their function. This chapter summarises events on aberrant DNA methylation, histone modifications, nucleosome positioning and non-coding RNA expression in human melanoma.

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References

  1. D’Mello SA, et al. Signaling pathways in Melanogenesis. Int J Mol Sci. 2016;17(7)

    Article  PubMed Central  CAS  Google Scholar 

  2. Besaratinia A, Tommasi S. Epigenetics of human melanoma: promises and challenges. J Mol Cell Biol. 2014;6(5):356–67.

    Article  PubMed  CAS  Google Scholar 

  3. Miller AJ, Mihm MC Jr. Melanoma. N Engl J Med. 2006;355(1):51–65.

    Article  PubMed  CAS  Google Scholar 

  4. Gray-Schopfer V, Wellbrock C, Marais R. Melanoma biology and new targeted therapy. Nature. 2007;445(7130):851–7.

    Article  PubMed  CAS  Google Scholar 

  5. Tsao H, et al. Melanoma: from mutations to medicine. Genes Dev. 2012;26(11):1131–55.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Ransohoff KJ, et al. Familial skin cancer syndromes: increased melanoma risk. J Am Acad Dermatol. 2016;74(3):423–34. quiz 435-6

    Article  PubMed  Google Scholar 

  7. Law MH, et al. Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma. Nat Genet. 2015;47(9):987–95.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Skolnick MH, Cannon-Albright LA, Kamb A. Genetic predisposition to melanoma. Eur J Cancer. 1994;30A(13):1991–5.

    Article  PubMed  CAS  Google Scholar 

  9. Wangari-Talbot J, Chen S. Genetics of melanoma. Front Genet. 2012;3:330.

    PubMed  Google Scholar 

  10. Sarkar D, et al. Epigenetic regulation in human melanoma: past and future. Epigenetics. 2015;10(2):103–21.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Youngson NA, Whitelaw E. Transgenerational epigenetic effects. Annu Rev Genomics Hum Genet. 2008;9:233–57.

    Article  PubMed  CAS  Google Scholar 

  12. Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol. 2010;28(10):1057–68.

    Article  PubMed  CAS  Google Scholar 

  13. Bestor T, et al. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J Mol Biol. 1988;203(4):971–83.

    Article  PubMed  CAS  Google Scholar 

  14. Rodger EJ, Chatterjee A, Morison IM. 5-hydroxymethylcytosine: a potential therapeutic target in cancer. Epigenomics. 2014;6(5):503–14.

    Article  PubMed  CAS  Google Scholar 

  15. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–92.

    Article  PubMed  CAS  Google Scholar 

  16. Vogelstein B, et al. Cancer genome landscapes. Science. 2013;339(6127):1546–58.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Kulis M, Esteller M. DNA methylation and cancer. Adv Genet. 2010;70:27–56.

    PubMed  Google Scholar 

  18. Liu S, et al. Identification of novel epigenetically modified genes in human melanoma via promoter methylation gene profiling. Pigment Cell Melanoma Res. 2008;21(5):545–58.

    Article  PubMed  CAS  Google Scholar 

  19. Muthusamy V, et al. Epigenetic silencing of novel tumor suppressors in malignant melanoma. Cancer Res. 2006;66(23):11187–93.

    Article  PubMed  CAS  Google Scholar 

  20. Hoon DS, et al. Profiling epigenetic inactivation of tumor suppressor genes in tumors and plasma from cutaneous melanoma patients. Oncogene. 2004;23(22):4014–22.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Lahtz C, et al. Methylation of PTEN as a prognostic factor in malignant melanoma of the skin. J Invest Dermatol. 2010;130(2):620–2.

    Article  PubMed  CAS  Google Scholar 

  22. Chatterjee A, et al. Tools and strategies for analysis of genome-wide and gene-specific DNA methylation patterns. Methods Mol Biol. 2017;1537:249–77.

    Article  PubMed  CAS  Google Scholar 

  23. Stockwell PA, et al. DMAP: differential methylation analysis package for RRBS and WGBS data. Bioinformatics. 2014;30(13):1814–22.

    Article  PubMed  CAS  Google Scholar 

  24. Chatterjee, A., et al., scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups. Epigenomics, 2016.

    Google Scholar 

  25. Seynnaeve B, et al. Genetic and epigenetic alterations of TERT are associated with inferior outcome in adolescent and young adult patients with melanoma. Sci Rep. 2017;7:45704.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Koga Y, et al. Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res. 2009;19(8):1462–70.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Conway K, et al. DNA-methylation profiling distinguishes malignant melanomas from benign nevi. Pigment Cell Melanoma Res. 2011;24(2):352–60.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Gao L, et al. Promoter CpG island hypermethylation in dysplastic nevus and melanoma: CLDN11 as an epigenetic biomarker for malignancy. J Invest Dermatol. 2014;134(12):2957–66.

    Article  PubMed  CAS  Google Scholar 

  29. Jin SG, et al. The DNA methylation landscape of human melanoma. Genomics. 2015;106(6):322–30.

    Article  PubMed  CAS  Google Scholar 

  30. Marzese DM, et al. Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis. Hum Mol Genet. 2014;23(1):226–38.

    Article  PubMed  CAS  Google Scholar 

  31. Lauss M, et al. DNA methylation subgroups in melanoma are associated with proliferative and immunological processes. BMC Med Genet. 2015;8:73.

    Google Scholar 

  32. Sigalotti L, et al. Whole genome methylation profiles as independent markers of survival in stage IIIC melanoma patients. J Transl Med. 2012;10:185.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Vizoso M, et al. Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR. Nat Med. 2015;21(7):741–50.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature. 1983;301(5895):89–92.

    Article  PubMed  CAS  Google Scholar 

  35. Guo X, Xu Y, Zhao Z. In-depth genomic data analyses revealed complex transcriptional and epigenetic dysregulations of BRAFV600E in melanoma. Mol Cancer. 2015;14:60.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Chatterjee A, et al. Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis. Oncotarget. 2017;8(4):6085–101.

    Article  PubMed  Google Scholar 

  37. Ross JP, Rand KN, Molloy PL. Hypomethylation of repeated DNA sequences in cancer. Epigenomics. 2010;2(2):245–69.

    Article  PubMed  CAS  Google Scholar 

  38. Ecsedi SI, et al. Transposable hypomethylation is associated with metastatic capacity of primary melanomas. Int J Clin Exp Pathol. 2013;6(12):2943–8.

    PubMed  PubMed Central  Google Scholar 

  39. Sigalotti L, et al. Promoter methylation controls the expression of MAGE2, 3 and 4 genes in human cutaneous melanoma. J Immunother. 2002;25(1):16–26.

    Article  PubMed  CAS  Google Scholar 

  40. Grunau C, et al. Frequent DNA hypomethylation of human juxtacentromeric BAGE loci in cancer. Genes Chromosomes Cancer. 2005;43(1):11–24.

    Article  PubMed  CAS  Google Scholar 

  41. Barrow C, et al. Tumor antigen expression in melanoma varies according to antigen and stage. Clin Cancer Res. 2006;12(3 Pt 1):764–71.

    Article  PubMed  CAS  Google Scholar 

  42. Gjerstorff MF, Andersen MH, Ditzel HJ. Oncogenic cancer/testis antigens: prime candidates for immunotherapy. Oncotarget. 2015;6(18):15772–87.

    Article  PubMed  PubMed Central  Google Scholar 

  43. Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011;11(10):726–34.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Mezzanotte JJ, et al. RASSF6 exhibits promoter hypermethylation in metastatic melanoma and inhibits invasion in melanoma cells. Epigenetics. 2014;9(11):1496–503.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Hallberg AR, et al. Aberrant CpG methylation of the TFAP2A gene constitutes a mechanism for loss of TFAP2A expression in human metastatic melanoma. Epigenetics. 2014;9(12):1641–7.

    Article  PubMed  Google Scholar 

  46. Aran D, Sabato S, Hellman A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol. 2013;14(3):R21.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Coppola CJ. C.R. R, and E.M. Mendenhall, Identification and function of enhancers in the human genome. Hum Mol Genet. 2016;25(R2):R190–7.

    Article  PubMed  CAS  Google Scholar 

  48. Bell RE, et al. Enhancer methylation dynamics contribute to cancer plasticity and patient mortality. Genome Res. 2016;26(5):601–11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Gallagher SJ, Tiffen JC, Hersey P. Histone modifications, modifiers and readers in melanoma resistance to targeted and immune therapy. Cancers (Basel). 2015;7(4):1959–82.

    Article  CAS  Google Scholar 

  50. Kouzarides T. Chromatin modifications and their function. Cell. 2007;128(4):693–705.

    Article  PubMed  CAS  Google Scholar 

  51. Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011;21(3):381–95.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Zhang Y, Reinberg D. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev. 2001;15(18):2343–60.

    Article  PubMed  CAS  Google Scholar 

  53. Lee MG, et al. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature. 2005;437(7057):432–5.

    Article  PubMed  CAS  Google Scholar 

  54. Fischle W, et al. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature. 2005;438(7071):1116–22.

    Article  PubMed  CAS  Google Scholar 

  55. Krishnamoorthy T, et al. Phosphorylation of histone H4 Ser1 regulates sporulation in yeast and is conserved in fly and mouse spermatogenesis. Genes Dev. 2006;20(18):2580–92.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. Shogren-Knaak M, et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science. 2006;311(5762):844–7.

    Article  PubMed  CAS  Google Scholar 

  57. Shogren-Knaak M, Peterson CL. Switching on chromatin - mechanistic role of histone H4-K16 acetylation. Cell Cycle. 2006;5(13):1361–5.

    Article  PubMed  CAS  Google Scholar 

  58. Nelson CJ, Santos-Rosa H, Kouzarides T. Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell. 2006;126(5):905–16.

    Article  PubMed  CAS  Google Scholar 

  59. Clements A, et al. Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferase. Mol Cell. 2003;12(2):461–73.

    Article  PubMed  CAS  Google Scholar 

  60. Zhao R, et al. Implications of genetic and epigenetic alterations of CDKN2A (p16(INK4a)) in cancer. EBioMedicine. 2016;8:30–9.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Konieczkowski DJ, et al. A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Cancer Discov. 2014;4(7):816–27.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  62. Wilmott JS, et al. Expression of the class 1 histone deacetylases HDAC8 and 3 are associated with improved survival of patients with metastatic melanoma. Mod Pathol. 2015;28(7):884–94.

    Article  PubMed  CAS  Google Scholar 

  63. Tiffen J, Gallagher SJ, Hersey P. EZH2: an emerging role in melanoma biology and strategies for targeted therapy. Pigment Cell Melanoma Res. 2015;28(1):21–30.

    Article  PubMed  CAS  Google Scholar 

  64. Barsotti AM, et al. Epigenetic reprogramming by tumor-derived EZH2 gain-of-function mutations promotes aggressive 3D cell morphologies and enhances melanoma tumor growth. Oncotarget. 2015;6(5):2928–38.

    Article  PubMed  PubMed Central  Google Scholar 

  65. Chen IP, et al. UVA-induced epigenetic regulation of P16(INK4a) in human epidermal keratinocytes and skin tumor derived cells. Photochem Photobiol Sci. 2012;11(1):180–90.

    Article  PubMed  CAS  Google Scholar 

  66. Mahmoud F, et al. Role of EZH2 histone methyltrasferase in melanoma progression and metastasis. Cancer Biol Ther. 2016;17(6):579–91.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Campos EI, et al. The novel tumour suppressor gene ING1 is overexpressed in human melanoma cell lines. Br J Dermatol. 2002;146(4):574–80.

    Article  PubMed  CAS  Google Scholar 

  68. Ondrusova L, et al. MITF-independent pro-survival role of BRG1-containing SWI/SNF complex in melanoma cells. PLoS One. 2013;8(1):e54110.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  69. Nikolaev SI, et al. A single-nucleotide substitution mutator phenotype revealed by exome sequencing of human colon adenomas. Cancer Res. 2012;72(23):6279–89.

    Article  PubMed  CAS  Google Scholar 

  70. Stark MS, et al. Frequent somatic mutations in MAP 3K5 and MAP 3K9 in metastatic melanoma identified by exome sequencing. Nat Genet. 2012;44(2):165–9.

    Article  CAS  Google Scholar 

  71. Wei XM, et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet. 2011;43(5):442–+.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  72. Hodis E, et al. A landscape of driver mutations in melanoma. Cell. 2012;150(2):251–63.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Vardabasso C, et al. Histone variants: emerging players in cancer biology. Cell Mol Life Sci. 2014;71(3):379–404.

    Article  PubMed  CAS  Google Scholar 

  74. Kapoor A, et al. The histone variant macroH2A suppresses melanoma progression through regulation of CDK8. Nature. 2010;468(7327):1105–9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  75. Duarte, L.F., et al., Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. Nat Commun, 2014. 5: p. 5210.

    Google Scholar 

  76. Mattick, J.S. and I.V. Makunin, Non-coding RNA. Hum Mol Genet, 2006. 15 Spec No 1: p. R17-29.

    Article  PubMed  CAS  Google Scholar 

  77. Mattick JS. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2001;2(11):986–91.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136(4):629–41.

    Article  PubMed  CAS  Google Scholar 

  79. Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell. 2009;136(4):642–55.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  80. Cech TR, Steitz JA. The noncoding RNA revolution-trashing old rules to forge new ones. Cell. 2014;157(1):77–94.

    Article  PubMed  CAS  Google Scholar 

  81. Cabili MN, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25(18):1915–27.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  82. Derrien T, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22(9):1775–89.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  83. Hung T, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet. 2011;43(7):621–9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  84. Mercer TR, et al. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A. 2008;105(2):716–21.

    Article  PubMed  PubMed Central  Google Scholar 

  85. Yan X, et al. Comprehensive genomic characterization of long non-coding RNAs across human cancers. Cancer Cell. 2015;28(4):529–40.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  86. Yoshimoto R, et al. MALAT1 long non-coding RNA in cancer. Biochim Biophys Acta. 2016;1859(1):192–9.

    Article  PubMed  CAS  Google Scholar 

  87. Ji P, et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene. 2003;22(39):8031–41.

    Article  PubMed  CAS  Google Scholar 

  88. Spector, D.L. and A.I. Lamond, Nuclear speckles. Cold Spring Harb Perspect Biol, 2011. 3(2).

    Google Scholar 

  89. Leucci E, et al. The emerging role of long non-coding RNAs in cutaneous melanoma. Pigment Cell Melanoma Res. 2016;29(6):619–26.

    Article  PubMed  CAS  Google Scholar 

  90. Wu L, et al. Binding interactions between long noncoding RNA HOTAIR and PRC2 proteins. Biochemistry. 2013;52(52):9519–27.

    Article  PubMed  CAS  Google Scholar 

  91. Kotake Y, et al. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene. 2011;30(16):1956–62.

    Article  PubMed  CAS  Google Scholar 

  92. Sato K, et al. ANRIL is implicated in the regulation of nucleus and potential transcriptional target of E2F1. Oncol Rep. 2010;24(3):701–7.

    PubMed  CAS  Google Scholar 

  93. Yap KL, et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell. 2010;38(5):662–74.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  94. Montes M, et al. The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence. Nat Commun. 2015;6:6967.

    Article  PubMed  CAS  Google Scholar 

  95. Ding X, et al. PAUPAR lncRNA suppresses tumourigenesis by H3K4 demethylation in uveal melanoma. FEBS Lett. 2016;590(12):1729–38.

    Article  PubMed  CAS  Google Scholar 

  96. Davidovich C, et al. Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. Mol Cell. 2015;57(3):552–8.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Tian Y, et al. Potential roles of abnormally expressed long noncoding RNA UCA1 and Malat-1 in metastasis of melanoma. Melanoma Res. 2014;24(4):335–41.

    Article  PubMed  CAS  Google Scholar 

  98. Wei Y, et al. LncRNA UCA1-miR-507-FOXM1 axis is involved in cell proliferation, invasion and G0/G1 cell cycle arrest in melanoma. Med Oncol. 2016;33(8):88.

    Article  PubMed  CAS  Google Scholar 

  99. Kruiswijk F, et al. Targeted inhibition of metastatic melanoma through interference with Pin1-FOXM1 signaling. Oncogene. 2016;35(17):2166–77.

    Article  PubMed  CAS  Google Scholar 

  100. Flockhart RJ, et al. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Res. 2012;22(6):1006–14.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Li R, et al. Long non-coding RNA BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation. PLoS One. 2014;9(6):e100893.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  102. Leucci E, et al. Melanoma addiction to the long non-coding RNA SAMMSON. Nature. 2016;531(7595):518–22.

    Article  PubMed  CAS  Google Scholar 

  103. Bachellerie JP, Cavaille J, Huttenhofer A. The expanding snoRNA world. Biochimie. 2002;84(8):775–90.

    Article  PubMed  CAS  Google Scholar 

  104. Weinstein LB, Steitz JA. Guided tours: from precursor snoRNA to functional snoRNP. Curr Opin Cell Biol. 1999;11(3):378–84.

    Article  PubMed  CAS  Google Scholar 

  105. Cavaille J, Bachellerie JP. SnoRNA-guided ribose methylation of rRNA: structural features of the guide RNA duplex influencing the extent of the reaction. Nucleic Acids Res. 1998;26(7):1576–87.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  106. Ganot P, Caizergues-Ferrer M, Kiss T. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 1997;11(7):941–56.

    Article  PubMed  CAS  Google Scholar 

  107. Kishore S, Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science. 2006;311(5758):230–2.

    Article  PubMed  CAS  Google Scholar 

  108. Ender C, et al. A human snoRNA with microRNA-like functions. Mol Cell. 2008;32(4):519–28.

    Article  PubMed  CAS  Google Scholar 

  109. Kishore S, et al. The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum Mol Genet. 2010;19(7):1153–64.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  110. Ono M, et al. Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res. 2011;39(9):3879–91.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  111. Chang LS, et al. Differential expression of human 5S snoRNA genes. Biochem Biophys Res Commun. 2002;299(2):196–200.

    Article  PubMed  CAS  Google Scholar 

  112. Donsante A, et al. AAV vector integration sites in mouse hepatocellular carcinoma. Science. 2007;317(5837):477.

    Article  PubMed  CAS  Google Scholar 

  113. Dong XY, et al. Implication of snoRNA U50 in human breast cancer. J Genet Genomics. 2009;36(8):447–54.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  114. Dong XY, et al. SnoRNA U50 is a candidate tumor-suppressor gene at 6q14.3 with a mutation associated with clinically significant prostate cancer. Hum Mol Genet. 2008;17(7):1031–42.

    Article  PubMed  CAS  Google Scholar 

  115. Tanaka R, et al. Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B-cell lymphoma. Genes Cells. 2000;5(4):277–87.

    Article  PubMed  CAS  Google Scholar 

  116. Askarian-Amiri ME, et al. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA. 2011;17(5):878–91.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  117. Liao J, et al. Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Mol Cancer. 2010;9:198.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  118. Mourtada-Maarabouni M, et al. Growth arrest in human T-cells is controlled by the non-coding RNA growth-arrest-specific transcript 5 (GAS5). J Cell Sci. 2008;121(Pt 7):939–46.

    Article  PubMed  CAS  Google Scholar 

  119. Mourtada-Maarabouni M, et al. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene. 2009;28(2):195–208.

    Article  PubMed  CAS  Google Scholar 

  120. Pickard MR, Mourtada-Maarabouni M, Williams GT. Long non-coding RNA GAS5 regulates apoptosis in prostate cancer cell lines. Biochim Biophys Acta. 2013;1832(10):1613–23.

    Article  PubMed  CAS  Google Scholar 

  121. Siprashvili Z, et al. The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer. Nat Genet. 2016;48(1):53–8.

    Article  PubMed  CAS  Google Scholar 

  122. Ichigozaki Y, et al. Serum long non-coding RNA, snoRNA host gene 5 level as a new tumor marker of malignant melanoma. Exp Dermatol. 2016;25(1):67–9.

    Article  PubMed  Google Scholar 

  123. Valencia-Sanchez MA, et al. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 2006;20(5):515–24.

    Article  PubMed  CAS  Google Scholar 

  124. Zhang L, et al. microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A. 2006;103(24):9136–41.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  125. Howell PM Jr, et al. MicroRNA in melanoma. Ochsner J. 2010;10(2):83–92.

    PubMed  PubMed Central  Google Scholar 

  126. Bemis LT, et al. MicroRNA-137 targets microphthalmia-associated transcription factor in melanoma cell lines. Cancer Res. 2008;68(5):1362–8.

    Article  PubMed  CAS  Google Scholar 

  127. Ozsolak F, et al. Chromatin structure analyses identify miRNA promoters. Genes Dev. 2008;22(22):3172–83.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  128. Dror, S., et al., Melanoma miRNA trafficking controls tumour primary niche formation. Nat Cell Biol, 2016. 18(9): p. 1006-17.

    Google Scholar 

  129. Lee JJ, et al. Targeted next-generation sequencing reveals high frequency of mutations in epigenetic regulators across treatment-naive patient melanomas. Clin Epigenetics. 2015;7:59.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  130. Pardoll DM. The blockade of immune checkpoints in cancer immunotherapy. Nat Rev Cancer. 2012;12(4):252–64.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  131. Robert C, et al. Pembrolizumab versus Ipilimumab in advanced melanoma. N Engl J Med. 2015;372(26):2521–32.

    Article  CAS  PubMed  Google Scholar 

  132. Dear AE. Epigenetic modulators and the new immunotherapies. N Engl J Med. 2016;374(7):684–6.

    Article  PubMed  CAS  Google Scholar 

  133. Wrangle J, et al. Alterations of immune response of non-small cell lung cancer with Azacytidine. Oncotarget. 2013;4(11):2067–79.

    Article  PubMed  PubMed Central  Google Scholar 

  134. Maio M, et al. Molecular pathways: at the crossroads of cancer epigenetics and immunotherapy. Clin Cancer Res. 2015;21(18):4040–7.

    Article  PubMed  CAS  Google Scholar 

  135. Chiappinelli KB, et al. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell. 2016;164(5):1073.

    Article  PubMed  CAS  Google Scholar 

  136. Chiappinelli KB, et al. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell. 2015;162(5):974–86.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  137. Jones PA, Issa JP, Baylin S. Targeting the cancer epigenome for therapy. Nat Rev Genet. 2016;17(10):630–41.

    Article  PubMed  CAS  Google Scholar 

  138. Poulikakos PI, Rosen N. Mutant BRAF melanomas--dependence and resistance. Cancer Cell. 2011;19(1):11–5.

    Article  PubMed  CAS  Google Scholar 

  139. Khvorova A, Watts JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol. 2017;35(3):238–48.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  140. Liang, X.H., et al., Translation efficiency of mRNAs is increased by antisense oligonucleotides targeting upstream open reading frames. Nature Biotechnology, 2016. 34(8): p. 875−+.

    Article  PubMed  CAS  Google Scholar 

  141. Lundin KE, Gissberg O, Smith CI. Oligonucleotide therapies: the past and the present. Hum Gene Ther. 2015;26(8):475–85.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  142. Witt O, et al. HDAC family: what are the cancer relevant targets? Cancer Lett. 2009;277(1):8–21.

    Article  PubMed  CAS  Google Scholar 

  143. Nathan D, Sterner DE, Berger SL. Histone modifications: now summoning sumoylation. Proc Natl Acad Sci U S A. 2003;100(23):13118–20.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  144. Koch-Nolte F, et al. Mammalian ADP-ribosyltransferases and ADP-ribosylhydrolases. Front Biosci. 2008;13:6716–29.

    Article  PubMed  CAS  Google Scholar 

  145. Moss J. A. Zolkiewska, and I. Okazaki, ADP-ribosylarginine hydrolases and ADP-ribosyltransferases. Partners in ADP-ribosylation cycles. Adv Exp Med Biol. 1997;419:25–33.

    Article  PubMed  CAS  Google Scholar 

  146. Pasmant E, et al. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res. 2007;67(8):3963–9.

    Article  PubMed  CAS  Google Scholar 

  147. Lessard L, et al. The CASC15 long Intergenic noncoding RNA locus is involved in melanoma progression and phenotype switching. J Invest Dermatol. 2015;135(10):2464–74.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Tang L, et al. Long noncoding RNA HOTAIR is associated with motility, invasion, and metastatic potential of metastatic melanoma. Biomed Res Int. 2013;2013:251098.

    PubMed  PubMed Central  Google Scholar 

  149. Wu CF, et al. The non-coding RNA llme23 drives the malignant property of human melanoma cells. J Genet Genomics. 2013;40(4):179–88.

    Article  PubMed  CAS  Google Scholar 

  150. Poliseno L, et al. Deletion of PTENP1 pseudogene in human melanoma. J Invest Dermatol. 2011;131(12):2497–500.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  151. Schmidt K, et al. The lncRNA SLNCR1 mediates melanoma invasion through a conserved SRA1-like region. Cell Rep. 2016;15(9):2025–37.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  152. Khaitan D, et al. The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res. 2011;71(11):3852–62.

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Marjan E. Askarian-Amiri Ph.D. .

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Askarian-Amiri, M.E., Rodger, E.J., Chatterjee, A., Finlay, G., Baguley, B.C. (2018). Epigenetics in Melanoma. In: Riker, A. (eds) Melanoma. Springer, Cham. https://doi.org/10.1007/978-3-319-78310-9_7

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