New perspectives of "omics" applications in melanoma research

Open Biochemistry Journal

Volumn 5, Issue , 2011, Pages 60-66

  Rodríguez Cerdeira, Carmen ^a   Molares Vila, Alberto ^b  

^a UNIVERSITY HOSPITAL COMPLEX OF VIGO   (Spain)

^b UNIVERSITY OF VIGO   (Spain)

Author keywords

Epigenetics; Genomics; Melanoma; MiRNA; Proteomics

Indexed keywords

CXCL14 CHEMOKINE; EPIDERMAL GROWTH FACTOR RECEPTOR 3; GENOMIC DNA; HEAT SHOCK PROTEIN 90; HISTONE DEACETYLASE; INHIBITOR OF GROWTH FAMILY MEMBER 3; INHIBITOR OF GROWTH FAMILY MEMBER 4; LACTATE DEHYDROGENASE; MAMMALIAN CHITINASE LIKE PROTEIN MEMBER YKL 40; MELANOMA INHIBITING ACTIVITY PROTEIN; MESSENGER RNA; MICRORNA; MICRORNA 200; MICRORNA 205; MINICHROMOSOME MAINTENANCE PROTEIN 4; MINICHROMOSOME MAINTENANCE PROTEIN 6; OPSIN; OSTEOPONTIN; PROTEIN S100B; RGS PROTEIN; RGS1 PROTEIN; STEROID RECEPTOR COACTIVATOR 3; TUMOR ASSOCIATED ANTIGEN 90 IMMUNE COMPLEX; TUMOR PROTEIN; UNCLASSIFIED DRUG; WNT5A PROTEIN;

ARTIFICIAL NEURAL NETWORK; CANCER RESEARCH; CELL DIVISION CONTROL PROTEIN 28 GENE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPLEX FORMATION; COPY NUMBER VARIATION; DESMOCOLLIN 3 GENE; DISEASE ACTIVITY; DNA MODIFICATION; DOWN REGULATION; EPIGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENETIC ASSOCIATION; GENOME ANALYSIS; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; INTERMETHOD COMPARISON; MARKER GENE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MELANOMA; METASTASIS; MICROARRAY ANALYSIS; NONHUMAN; OUTCOME ASSESSMENT; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROGNOSIS; PROMOTER REGION; PROTEOMICS; REVIEW; TANDEM MASS SPECTROMETRY; TUMOR GROWTH;

EID: 84855720599     PISSN: None     EISSN: 1874091X     Source Type: Journal    
DOI: 10.2174/1874091X01105010060     Document Type: Review

References (51)

1. Marugame, T.; Zhang, M.J. Comparison of time trends in melanoma of skin cancer mortality (1990-2006) between countries based on the WHO mortality database. Jpn. J. Clin. Oncol,. 2010, 40, 710.
2. Algaza, A.P.; Soon, C.W.; Daud, A.I. Treatment of cutaneous melanoma: current approaches and future prospects. Cancer Manag. Res., 2010, 2, 197-211.
3. Davies, H.; Bignell, G.R.; Cox, C.; Stephens, P.; Edkins, S.; Clegg, S.; Teague, J.; Woffendin, H.; Garnett, M.J.; Bottomley, W.; Davis, N.; Dicks, E.; Ewing, R.; Floyd, Y.; Gray, K.; Hall, S.; Hawes, R.; Hughs, J.; Kosmidou, V.; Menzies, A.; Mould, C.; Parker, A.; Stevens, C.; Watt, S.; Hooper, S.; Wilson, R.; Jayatilake, H.; Gusterson, B.A.; Cooper, C.; Shipley, J.; Hargrave, D.; Pritchard-Jones, K.; Maitland, N.; Chenevix-Trench, G.; Riggins, G.J.; Bigner, D.D.; Palmieri, G.; Cossu, A.; Flanagan A, Nicholson, A.; Ho, J.W.; Leung, S.Y.; Yuen, S.T; Weber, B.L.; Seigler, H.F.; Darrow, T.L.; Paterson, H.; Marais, R.; Marshall, C.J.; Wooster, R.; Stratton, M.R.; Futreal, P.A. Mutations of the BRAF gene in human cancer. Nature, 2002, 417, 949-954.
4. Palmieri, G.; Capone, M.; Ascierto, M.L.; Gentilcore, G.; Stroncek, D.F.; Casula, M.; Sini, M.C.; Palla, M.; Mozzillo, N.; Ascierto, P.A. Main roads to melanoma. J. Transl. Med., 2009, 7, 86.
5. Di Micco, R.; Cicalese, A.; Fumagalli, M.; Dobreva, M.; Verrecchia, A.; Pelicci, P.J. DNA damage response activation in mouse embryonic fibroblasts undergoing replicative senescence and following spontaneous immortalization. Cell Cycle, 2008, 7, 3601-3606.
6. Thompson, J.F.; Scolyer, R.A.; Kefford, R.F.;. Cutaneous melanoma. Lancet, 2005, 365, 687-701.
7. Haluska, F.G.; Tsao, H.; Wu, H.; Haluska, F.S.; Lazar, A.; Goel, V. Genetic alterations in signaling pathways in melanoma. Clin. Cancer Res., 2006, 12, 2301s-2307s.
8. Soengas, M.S; Lowe, S.W. Apoptosis and melanoma chemoresistance. Oncogene, 2003, 22, 3138-3151.
9. Tímár, J.; Gyorffy, B.; Rásó, E. Gene signature of the metastatic potential of cutaneous melanoma: too much for too little? Clin. Exp. Metastasis, 2010, 27, 371-87.
10. Jaeger, J.; Koczan, D.; Thiesen, H.; Ibrahim, S.M.; Gross, G.; Span, R.; Kunz, M. Gene expression signatures for tumor progression, tumor subtype, and tumor thickness in laser-microdissected melanoma tissues. Clin. Cancer Res., 2007, 13, 806-815.
11. Schmitt, C.J.; Franke, W.W.; Goerdt, S.; Falkowska-Hansen, B.; Rickelt, S.; Peitsch, W.R. Homo and heterotypic cell contacts in malignant melanoma cells and desmoglein 2 as a novel solitary surface glycoprotein. J. Invest. Dermatol., 2007, 127, 2191-2206.
12. Ross, D.A.; Laing, J.H.E.; Sanders, R.; Wilson, G.D. Long term follow-up of c-myc, p53 and proliferation measurements in malignant melanoma. Eur. J. Surg. Oncol., 2006, 32, 80-84.
13. Akslen, L.A.; Puntervoll, H.; Bachmann, I.M.; Straume, O.: Vuhahula., E. Mutation analysis of the EGFR-NRAS-BRAF pathway in melanomas from black Africans and other subgroups of cutaneous melanoma. Melanoma Res., 2008, 18, 29-35.
14. Maelandsmo, G.M.; Flørenes, V.A.; Mellingsaeter, T.; Hovig, E.; Kerbel, R.S. Differential expression patterns of S100A2, S100A4 and S100A6 during progression of human malignant melanoma. Int. J. Cancer, 1997, 74, 464-469.
15. Steeg, P.S. Tumor metastasis: mechanistic insights and clinical challenges. Nat. Med., 2006, 12, 895-904.
16. Hilmi, C.; Larribere, L.; Giuliano, S.; Bille, K.; Ortonne, J.; Ballotti, R. Bertolotto, C. IGF1 promotes resistance to apoptosis in melanoma cells through an increased expression of BCL2, BCL-X(L), and survivin. J. Invest. Dermatol., 2008, 128, 1499-1505.
17. Packer, L.; Pavey, S.; Parker, A.; Stark, M.; Johansson, P.; Clarke, B. Osteopontin is a downstream effector of the PI3-kinase pathway in melanomas that is inversely correlated with functional PTEN. Carcinogenesis, 2006, 27, 1778-86.
18. Gerami, P.; Jewell, S.S.; Morrison, L.E.; Blondin, B.; Schulz, J.; Ruffalo, T., Obenauf, A.C; Wackernagel, W.; Green, G.; Bouvier, N.; Sozen, M.M.; Baimukanova, G.; Roy, R.; Heguy, A.; Dolgalev, I.; Khanin, R.; Busam, K.; Speicher, M.R.; O'Brien, J.; Bastian, B.C. Fluorescence in situ hybridization (FISH) as an ancillary diagnostic tool in the diagnosis of melanoma. Am. J. Surg. Pathol., 2009, 33, 1146-1156.
19. Bastian, B.C.; Xiong, J.; Frieden, I.J.; Williams, M.L.; Chou, P.; Busam, K.; Pinkel, D.; LeBoit, P.E. Genetic changes in neoplasms arising in congenital melanocytic nevi: differences between nodular proliferations and melanomas. Am. J. Pathol., 2002, 161, 1163-1169.
20. van Dijk, M.C.; Bernsen, M.R.; Ruiter, D.M.J. Analysis of mutations in B-RAF, N-RAS, and H-RAS genes in the differential diagnosis of Spitz nevus and spitzoid melanoma. Am. J. Surg. Pathol., 2005, 29, 1145-1151.
21. North, J.P.; Kageshita, T.; Pinkel, D.; LeBoit, P.E.; Bastian, B.C. Distribution and significance of occult intraepidermal tumor cells surrounding primary melanoma. J. Invest. Dermatol., 2008, 128, 2024-2030.
22. Winnepenninckx, V.; Lazar, V.; Michiels, S.; Dessen, P.; Stas, M.; Alonso, S.R.; Avril, M.F.; Ortiz- Romero, P.L.; Robert, T.; Balacescu, O.; Eggermont, A.M.; Lenoir, G.; Sarasin, A.; Tursz, T.; van den Oord, J.J.; Spatz, A. Melanoma Group of the European Organization for Research and Treatment of Cancer. Gene expression profiling of primary cutaneous melanoma and clinical outcome. J. Natl. Cancer Inst., 2006, 98, 472-482.
23. Pearl, R.A.; Pacifico, M.D.; Richman, P.I.; Stott, D.J.; Wilson, G.D.; Grobbelaar, A.O. Ki-67 expression in melanoma. A potential method of risk assessment for the patient with a positive sentinel node. J. Exp. Clin. Cancer Res., 2007, 26, 109-115.
24. Elliott, B.; Scolyer, R.A.; Suciu, S.; Lebecque, S.; Rimoldi, D.; Gugerli, O.; Musat, E.; Sharma, R.N.; Lienard, D.; Keilholz, U.; Testori, A.; Eggermont, A.; MacKie, R.; Robert, C.; Cook, M.; Thompson, J.F.; Angevin, E.; Spatz, A. European Organization for Research and Treatment of Cancer Melanoma Group. Long-term protective effect of mature DC-LAMP+ dendritic cell accumulation in sentinel lymph nodes containing micrometastatic melanoma. Clin. Cancer Res., 2007; 13: 3825-30.
25. Eggermont, A.M.; Suciu, S.; Santinami, M.; Testori, A.; Kruit, W.H. Adjuvant therapy with pegylated interferon alfa-2b versus observation alone in resected stage III melanoma: final results of EORTC 18991, a randomised phase III trial. Lancet, 2008, 372, 117-126.
26. Van den Oord, J.J.; Sarasin, A.; Winnepenninckx, V.; Spatz, A. Expression profiling of melanoma cell lines: in search of a progression related molecular signature. Future Onco., 2007, 3, 609-611.
27. Winnepenninckx, V.; Debiec-Rychter, M.; Beliën, J.A.; Fiten, P.; Michiels, S.; Lazar, V.; Opdenakker, G.; Meijer, G.A.; Spatz, A.; van den Oord, J.J. Expression and possible role of hPTTG1/securing in cutaneous malignant melanoma. Mod. Pathol., 2006, 19, 1170-1180.
28. Gogas, H.; Eggermont, A.M.; Hauschild, A.; Hersey, P.; Mohr, P.; Schadendorf, D. Biomarkers in melanoma. Ann. Oncol., 2009, 20 Suppl 6, vi8-13.
29. Howell, P.M.; Liu, S.; Ren, S.; Behlen, C.; Fodstad, O.; Riker, A.I. Epigenetics in human melanoma. Cancer Control, 2009, 16, 200-218.
30. Liu, S.; Ren, S.; Howell, P.; Fodstad, O.; Riker, A.I. Identification of novel epigenetically modified genes in human melanoma via promoter methylation gene profiling. Pigment Cell Melanoma Res., 2008, 21, 545-558.
31. Luo, W.; Wang, X.; Kageshita, T.; Wakasugi, S.; Karpf, A.R.; Ferrone, S. Regulation of high molecular weight-melanoma associated antigen (HMW-MAA) gene expression by promoter DNA methylation in human melanoma cells. Oncogene, 2006, 25, 2873-2884.
32. James, S.R.; Link, P.A.; Karpf, A.R. Epigenetic regulation of Xlinked cancer/germline antigen genes by DNMT1 and DNMT3b. Oncogene, 2006, 25: 6975-6985.
33. Li, J.; Martinka, M.; Li, G. Role of ING4 in human melanoma cell migration, invasion and patient survival. Carcinogenesis, 2008, 29, 1373-1379.
34. Wang, Y.; Dai, D.L.; Martinka, M.; Li, G. Prognostic significance of nuclear ING3 expression in human cutaneous melanoma. Clin. Cancer Res., 2007, 13, 4111-4116.
35. Zhuang, D.; Mannava, S.; Grachtchouk, V.; Tang, W.; Patil, S.; Wawrzyniak, J.A.; Berman, A.E.; Giordano, T.J.; Prochownik, E.V.; Soengas, M.S.; Nikiforov, M.A. C-MYC overexpression is required for continuous suppression of oncogene-induced senescence in melanoma cells. Oncogene, 2008, 27, 6623-6634.
36. Garraway, L.A.; Widlund, H.R.; Rubin, M.A.; Getz, G.; Berger, A.J.; Ramaswamy, S.; Beroukhim, R.; Milner, D.A.; Granter, S.R.; Du, J.; Lee, C.; Wagner, S.N.; Li, C.; Golub, T.R.; Rimm, D.L.; Meyerson, M.L.; Fisher, D.E.; Sellers, W.R. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature, 2005, 436, 117-122.
37. Dynek, J.N.; Chan, S.M.; Liu, J.; Zha, J.; Fairbrother, W.J.; Vucic, D. Microphthalmia-associated transcription factor is a critical transcriptional regulator of melanoma inhibitor of apoptosis in melanomas. Cancer Res., 2008, 68, 3124-3132.
38. Lomas, J.; Martin-Duque, P.; Pons, M.; Quintanilla, M. The genetics of malignant melanoma. Front. Biosci., 2008, 13, 5071-5093.
39. Ugurel, S.; Houben, R.; Schrama, D.; Voigt, H.; Zapatka, M.; Schadendorf, D.; Bröcker, E.B.; Becker, J.C. Microphthalmiaassociated transcription factor gene amplification in metastatic melanoma is a prognostic marker for patient survival, but not a predictive marker for chemosensitivity and chemotherapy response. Clin. Cancer Res., 2007, 13, 6344-6350.
40. Riker, A.I.; Enkemann, S.A.; Fodstad, O.; Liu, S.; Ren, S.; Morris., C.; Howell, P.; Metge, B.; Samant, R.S.; Shevde, L.A.; Li, W.; Eschrich, S.; Daud, A.; Ju, J.; Matta, J. The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis. BMC Med. Genomics, 2008, 1, 13.
41. Bonazzi, V.F.; Irwin, D.; Hayward, N.K. Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma. Genes Chromosomes Cancer, 2009, 48, 10-21.
42. Yi, R.; Fuchs, E. MicroRNA-mediated control in the skin. Cell Death Differ., 2010, 17, 229-235.
43. Childs, G.; Fazzari, M.; Kung, G.; Kawachi, N.; Brandwein-Gensler, M.; McLemore, M.; McLemore, M.; Chen, Q.; Burk, R.D.; Smith, R.V.; Prystowsky, M.B.; Belbin, T.J.; Schlecht, N.F. Low-level expression of microRNAs let-7d and miR-205 are prognostic markers of head and neck squamous cell carcinoma. Am. J. Pathol., 2009, 174, 736-745.
44. Yu, J.; Ryan, D.G.; Getsios, S.; Oliveira-Fernandes, M.; Fatima, A.; Lavker, R.M. MicroRNA-184 antagonizes microRNA-205 to maintain SHIP2 levels in epithelia. Proc. Natl. Acad. Sci. USA, 2008, 105, 19300-19305.
45. Mueller, D.W.; Bosserhoff, A.K. Role of miRNAs in the progression of malignant melanoma. Br. J. Cancer, 2009, 101, 551-556.
46. Mueller, D.W.; Rehli, M.; Bosserhoff, A.K. miRNA expression profiling in melanocytes and melanoma cell lines reveals miRNAs associated with formation and progression of malignant melanoma. J. Invest. Dermatol., 2009, 129, 1740-1751.
47. Segura, M.F.; Hanniford, D.; Menendez, S.; Reavie, L.; Zou, X.; Alvarez-Diaz, S. Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmiaassociated transcription factor. Proc. Natl. Acad. Sci. USA, 2009, 106, 1814-1819.
48. Mian, S.; Ugurel, S.; Parkinson, E.; Schlenzka, I.; Dryden, I.; Lacashire, L.; Ball, G.; Creaser, C.; Rees, R.; Schadendorf, D. Serum proteomic fingerprinting discriminates between clinical stages and predicts disease progression in melanoma patients. J. Clin. Oncol., 2005, 23, 5088-5093.
49. Findeisen, P.; Zapatka, M.; Peccerella, T.; Matzk, H.; Neumaier, M.; Schanderdorf, D.; Ugurel, S. Serum amyloid A as a prognostic marker in melanoma identified by proteomic profiling. J. Clin. Oncol., 2009, 27, 2199-2208.
50. Hu, L.; Ye, M.; Jiang, X.; Feng, S; Zou, H. Advances in hyphenated analytical techniques for shotgun proteome and peptidome analysis-a review. Anal. Chim. Acta., 2007, 598, 193-204.
51. Solassol, J.; Mangé, A. Identification of serum melanoma progression biomarkers through proteomic-based approaches. Expert Rev. Proteomics, 2009, 6, 341-343.