Advertisement

Cell and Tissue Research

, Volume 351, Issue 1, pp 85–98 | Cite as

Comparative microarray analysis of microRNA expression profiles in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases, and benign melanocytic nevi

  • Michael SandEmail author
  • Marina Skrygan
  • Daniel Sand
  • Dimitrios Georgas
  • Thilo Gambichler
  • Stephan A. Hahn
  • Peter Altmeyer
  • Falk G. Bechara
Regular Article

Abstract

Perturbations in microRNA (miRNA) expression profiles have been reported for cutaneous malignant melanoma (CMM) predominantly when examined in cell lines. Despite the rapidly growing number of newly discovered human miRNA sequences, the availability of up-to-date miRNA expression profiles for clinical samples of primary cutaneous malignant melanoma (PCMM), cutaneous malignant melanoma metastases (CMMM), and benign melanocytic nevi (BMN) is limited. Specimens excised from the center of tumors (lesional) from patients with PCMM (n=9), CMMM (n=4), or BMN (n=8) were obtained during surgery. An exploratory microarray analysis was performed by miRNA expression profiling based on Agilent platform screening for 1205 human miRNAs. The results from the microarray analysis were validated by TaqMan quantitative real-time polymerase chain reaction. In addition to several miRNAs previously known to be associated with CMM, 19 unidentified miRNA candidates were found to be dysregulated in CMM patient samples. Among the 19 novel miRNA candidates, the genes hsa-miR-22, hsa-miR-130b, hsa-miR-146b-5p, hsa-miR-223, hsa-miR-301a, hsa-miR-484, hsa-miR-663, hsa-miR-720, hsa-miR-1260, hsa-miR-1274a, hsa-miR-1274b, hsa-miR-3663-3p, hsa-miR-4281, and hsa-miR-4286 were upregulated, and the genes hsa-miR-24-1*, hsa-miR-26a, hsa-miR-4291, hsa-miR-4317, and hsa-miR-4324 were downregulated. The results of this study partially confirm previous CMM miRNA profiling studies identifying miRNAs that are dysregulated in CMM. However, we report several novel miRNA candidates in CMM tumors; these miRNA sequences require further validation and functional analysis to evaluate whether they play a role in the pathogenesis of CMM.

Keywords

microRNA Microarray Melanoma Melanoma metastases Benign melanocytic nevi Human 

Notes

Acknowledgements

The authors are grateful to Dr. Cornelia Graf and Stefan Kotschote, MS, for technical advice.

References

  1. Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355PubMedCrossRefGoogle Scholar
  2. Asangani IA, Rasheed SA, Nikolova DA, Leupold JH, Colburn NH, Post S, Allgayer H (2008) MicroRNA-21 (miR-21) post-transcriptionally downregulates tumor suppressor Pdcd4 and stimulates invasion, intravasation and metastasis in colorectal cancer. Oncogene 27:2128–2136PubMedCrossRefGoogle Scholar
  3. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297PubMedCrossRefGoogle Scholar
  4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57:289–300Google Scholar
  5. Bonazzi VF, Irwin D, Hayward NK (2009) Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma. Genes Chromosomes Cancer 48:10–21PubMedCrossRefGoogle Scholar
  6. Bonazzi VF, Stark MS, Hayward NK (2012) MicroRNA regulation of melanoma progression. Melanoma Res 22:101–113PubMedCrossRefGoogle Scholar
  7. Boone B, Jacobs K, Ferdinande L, Taildeman J, Lambert J, Peeters M, Bracke M, Pauwels P, Brochez L (2011) EGFR in melanoma: clinical significance and potential therapeutic target. J Cutan Pathol 38:492–502PubMedCrossRefGoogle Scholar
  8. Busse A, Keilholz U (2011) Role of TGF-beta in melanoma. Curr Pharm Biotechnol 12:2165–2175PubMedCrossRefGoogle Scholar
  9. Caramuta S, Egyhazi S, Rodolfo M, Witten D, Hansson J, Larsson C, Lui WO (2010) MicroRNA expression profiles associated with mutational status and survival in malignant melanoma. J Invest Dermatol 130:2062–2070PubMedCrossRefGoogle Scholar
  10. Chan E, Patel R, Nallur S, Ratner E, Bacchiocchi A, Hoyt K, Szpakowski S, Godshalk S, Ariyan S, Sznol M, Halaban R, Krauthammer M, Tuck D, Slack FJ, Weidhaas JB (2011) MicroRNA signatures differentiate melanoma subtypes. Cell Cycle 10:1845–1852PubMedCrossRefGoogle Scholar
  11. Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210PubMedCrossRefGoogle Scholar
  12. Elson-Schwab I, Lorentzen A, Marshall CJ (2010) MicroRNA-200 family members differentially regulate morphological plasticity and mode of melanoma cell invasion. PLoS One 5:pii:e13176CrossRefGoogle Scholar
  13. Fan T, Jiang S, Chung N, Alikhan A, Ni C, Lee CC, Hornyak TJ (2011) EZH2-dependent suppression of a cellular senescence phenotype in melanoma cells by inhibition of p21/CDKN1A expression. Mol Cancer Res 9:418–429PubMedCrossRefGoogle Scholar
  14. Faraoni I, Antonetti FR, Cardone J, Bonmassar E (2009) miR-155 gene: a typical multifunctional microRNA. Biochim Biophys Acta 1792:497–505PubMedCrossRefGoogle Scholar
  15. Frankel LB, Christoffersen NR, Jacobsen A, Lindow M, Krogh A, Lund AH (2008) Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J Biol Chem 283:1026–1033PubMedCrossRefGoogle Scholar
  16. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105PubMedCrossRefGoogle Scholar
  17. Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, Chen C, Ambros VR, Israel MA (2007) Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67:2456–2468PubMedCrossRefGoogle Scholar
  18. Geraldo MV, Yamashita AS, Kimura ET (2012) MicroRNA miR-146b-5p regulates signal transduction of TGF-beta by repressing SMAD4 in thyroid cancer. Oncogene 31:1910–1922PubMedCrossRefGoogle Scholar
  19. Glud M, Rossing M, Hother C, Holst L, Hastrup N, Nielsen FC, Gniadecki R, Drzewiecki KT (2010) Downregulation of miR-125b in metastatic cutaneous malignant melanoma. Melanoma Res 20:479–484PubMedCrossRefGoogle Scholar
  20. Grignol V, Fairchild ET, Zimmerer JM, Lesinski GB, Walker MJ, Magro CM, Kacher JE, Karpa VI, Clark J, Nuovo G, Lehman A, Volinia S, Agnese DM, Croce CM, Carson WE 3rd (2011) miR-21 and miR-155 are associated with mitotic activity and lesion depth of borderline melanocytic lesions. Br J Cancer 105:1023–1029PubMedCrossRefGoogle Scholar
  21. Howell PM Jr, Li X, Riker AI, Xi Y (2010) MicroRNA in melanoma. Ochsner J 10:83–92PubMedGoogle Scholar
  22. Igoucheva O, Alexeev V (2009) MicroRNA-dependent regulation of cKit in cutaneous melanoma. Biochem Biophys Res Commun 379:790–794PubMedCrossRefGoogle Scholar
  23. Jiang L, Lv X, Li J, Li X, Li W, Li Y (2012) The status of microRNA-21 expression and its clinical significance in human cutaneous malignant melanoma. Acta Histochem 114:582–588PubMedCrossRefGoogle Scholar
  24. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37:D98–D104PubMedCrossRefGoogle Scholar
  25. Jukic DM, Rao UN, Kelly L, Skaf JS, Drogowski LM, Kirkwood JM, Panelli MC (2010) MicroRNA profiling analysis of differences between the melanoma of young adults and older adults. J Transl Med 8:27PubMedCrossRefGoogle Scholar
  26. Karube Y, Tanaka H, Osada H, Tomida S, Tatematsu Y, Yanagisawa K, Yatabe Y, Takamizawa J, Miyoshi S, Mitsudomi T, Takahashi T (2005) Reduced expression of Dicer associated with poor prognosis in lung cancer patients. Cancer Sci 96:111–115PubMedCrossRefGoogle Scholar
  27. Katakowski M, Zheng X, Jiang F, Rogers T, Szalad A, Chopp M (2010) MiR-146b-5p suppresses EGFR expression and reduces in vitro migration and invasion of glioma. Cancer Invest 28:1024–1030PubMedCrossRefGoogle Scholar
  28. Katoh Y, Katoh M (2008) Hedgehog signaling, epithelial-to-mesenchymal transition and miRNA (review). Int J Mol Med 22:271–275PubMedGoogle Scholar
  29. Lee YS, Kim HK, Chung S, Kim KS, Dutta A (2005) Depletion of human micro-RNA miR-125b reveals that it is critical for the proliferation of differentiated cells but not for the down-regulation of putative targets during differentiation. J Biol Chem 280:16635–16641PubMedCrossRefGoogle Scholar
  30. Leidinger P, Keller A, Borries A, Reichrath J, Rass K, Jager SU, Lenhof HP, Meese E (2010) High-throughput miRNA profiling of human melanoma blood samples. BMC Cancer 10:262PubMedCrossRefGoogle Scholar
  31. Lesinski GB, Raig ET, Zimmerer JM, Karpa V, Nuovo G, Lehman A, Peters S, Kacher JE, Magro CM, Croce CM, Carson WE (2008) Micro-RNA-21 and micro-RNA-155 as predictors of a malignant phenotype in melanocytic lesions. J Clin Oncol 26:9001Google Scholar
  32. Levati L, Alvino E, Pagani E, Arcelli D, Caporaso P, Bondanza S, Di Leva G, Ferracin M, Volinia S, Bonmassar E, Croce CM, D'Atri S (2009) Altered expression of selected microRNAs in melanoma: antiproliferative and proapoptotic activity of miRNA-155. Int J Oncol 35:393–400PubMedGoogle Scholar
  33. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20PubMedCrossRefGoogle Scholar
  34. Lu Z, Li Y, Takwi A, Li B, Zhang J, Conklin DJ, Young KH, Martin R (2011) miR-301a as an NF-kappaB activator in pancreatic cancer cells. EMBO J 30:57–67PubMedCrossRefGoogle Scholar
  35. McHugh JB, Fullen DR, Ma L, Kleer CG, Su LD (2007) Expression of polycomb group protein EZH2 in nevi and melanoma. J Cutan Pathol 34:597–600PubMedCrossRefGoogle Scholar
  36. Meng F, Henson R, Wehbe-Janek H, Ghoshal K, Jacob ST, Patel T (2007) MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer. Gastroenterology 133:647–658PubMedCrossRefGoogle Scholar
  37. miRBase (2012) http://www.mirbase.org/
  38. Molnar V, Tamasi V, Bakos B, Wiener Z, Falus A (2008) Changes in miRNA expression in solid tumors: an miRNA profiling in melanomas. Semin Cancer Biol 18:111–122PubMedCrossRefGoogle Scholar
  39. Müller DW, Bosserhoff AK (2008) Integrin beta 3 expression is regulated by let-7a miRNA in malignant melanoma. Oncogene 27:6698–6706PubMedCrossRefGoogle Scholar
  40. Mueller DW, Bosserhoff AK (2009) Role of miRNAs in the progression of malignant melanoma. Br J Cancer 101:551–556PubMedCrossRefGoogle Scholar
  41. Mueller DW, Bosserhoff AK (2011) miRNAs in malignant melanoma. In: Bosserhoff AK (ed) Melanoma development: molecular biology genetics and clinical application. Springer, New York, pp 105–136Google Scholar
  42. Mueller DW, Rehli M, Bosserhoff AK (2009) miRNA expression profiling in melanocytes and melanoma cell lines reveals miRNAs associated with formation and progression of malignant melanoma. J Invest Dermatol 129:1740–1751PubMedCrossRefGoogle Scholar
  43. Nguyen T, Kuo C, Nicholl MB, Sim MS, Turner RR, Morton DL, Hoon DS (2011) Downregulation of microRNA-29c is associated with hypermethylation of tumor-related genes and disease outcome in cutaneous melanoma. Epigenetics 6:388–394PubMedCrossRefGoogle Scholar
  44. Philippidou D, Schmitt M, Moser D, Margue C, Nazarov PV, Muller A, Vallar L, Nashan D, Behrmann I, Kreis S (2010) Signatures of microRNAs and selected microRNA target genes in human melanoma. Cancer Res 70:4163–4173PubMedCrossRefGoogle Scholar
  45. Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet 2:418–427PubMedCrossRefGoogle Scholar
  46. Sand M, Gambichler T, Sand D, Skrygan M, Altmeyer P, Bechara FG (2009) MicroRNAs and the skin: tiny players in the body's largest organ. J Dermatol Sci 53:169–175PubMedCrossRefGoogle Scholar
  47. Sand M, Gambichler T, Sand D, Altmeyer P, Stuecker M, Bechara FG (2011) Immunohistochemical expression patterns of the microRNA-processing enzyme Dicer in cutaneous malignant melanomas, benign melanocytic nevi and dysplastic melanocytic nevi. Eur J Dermatol 21:18–21PubMedGoogle Scholar
  48. Sand M, Skrygan M, Georgas D, Sand D, Gambichler T, Altmeyer P, Bechara FG (2012) The miRNA machinery in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases and benign melanocytic nevi. Cell Tissue Res 350(1):119–26Google Scholar
  49. Sander S, Bullinger L, Klapproth K, Fiedler K, Kestler HA, Barth TF, Moller P, Stilgenbauer S, Pollack JR, Wirth T (2008) MYC stimulates EZH2 expression by repression of its negative regulator miR-26a. Blood 112:4202–4212PubMedCrossRefGoogle Scholar
  50. Satzger I, Mattern A, Kuettler U, Weinspach D, Voelker B, Kapp A, Gutzmer R (2010) MicroRNA-15b represents an independent prognostic parameter and is correlated with tumor cell proliferation and apoptosis in malignant melanoma. Int J Cancer 126:2553–2562PubMedGoogle Scholar
  51. Schultz J, Lorenz P, Gross G, Ibrahim S, Kunz M (2008) MicroRNA let-7b targets important cell cycle molecules in malignant melanoma cells and interferes with anchorage-independent growth. Cell Res 18:549–557PubMedCrossRefGoogle Scholar
  52. Segura MF, Belitskaya-Levy I, Rose AE, Zakrzewski J, Gaziel A, Hanniford D, Darvishian F, Berman RS, Shapiro RL, Pavlick AC, Osman I, Hernando E (2010) Melanoma microRNA signature predicts post-recurrence survival. Clin Cancer Res 16:1577–1586PubMedCrossRefGoogle Scholar
  53. Sheng Y, Engstrom PG, Lenhard B (2007) Mammalian microRNA prediction through a support vector machine model of sequence and structure. PLoS One 2:e946PubMedCrossRefGoogle Scholar
  54. Sigalotti L, Covre A, Fratta E, Parisi G, Colizzi F, Rizzo A, Danielli R, Nicolay HJ, Coral S, Maio M (2010) Epigenetics of human cutaneous melanoma: setting the stage for new therapeutic strategies. J Transl Med 8:56PubMedCrossRefGoogle Scholar
  55. Sokal R, Michener C (1958) A statistical method for evaluating systematic relationships. Univ Kans Sci Bull 38:1409–1438Google Scholar
  56. Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y, Mitsudomi T, Takahashi T (2004) Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 64:3753–3756PubMedCrossRefGoogle Scholar
  57. Thompson KL, Pine PS, Rosenzweig BA, Turpaz Y, Retief J (2007) Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA. BMC Biotechnol 7:57PubMedCrossRefGoogle Scholar
  58. Ueda Y, Richmond A (2006) NF-kappaB activation in melanoma. Pigment Cell Res 19:112–124PubMedCrossRefGoogle Scholar
  59. Wit PE de, Moretti S, Koenders PG, Weterman MA, Muijen GN van, Gianotti B, Ruiter DJ (1992) Increasing epidermal growth factor receptor expression in human melanocytic tumor progression. J Invest Dermatol 99:168–173Google Scholar
  60. Xu Y, Brenn T, Brown ER, Doherty V, Melton DW (2012) Differential expression of microRNAs during melanoma progression: miR-200c, miR-205 and miR-211 are downregulated in melanoma and act as tumour suppressors. Br J Cancer 106:553–561PubMedCrossRefGoogle Scholar
  61. Yang C, Wei W (2011) The miRNA expression profile of the uveal melanoma. Sci China Life Sci 54:351–358PubMedCrossRefGoogle Scholar
  62. Yang CH, Yue J, Pfeffer SR, Handorf CR, Pfeffer LM (2011) MicroRNA miR-21 regulates the metastatic behavior of B16 melanoma cells. J Biol Chem 286:39172–39178PubMedCrossRefGoogle Scholar
  63. Yeung ML, Yasunaga J, Bennasser Y, Dusetti N, Harris D, Ahmad N, Matsuoka M, Jeang KT (2008) Roles for microRNAs, miR-93 and miR-130b, and tumor protein 53-induced nuclear protein 1 tumor suppressor in cell growth dysregulation by human T-cell lymphotrophic virus 1. Cancer Res 68:8976–8985PubMedCrossRefGoogle Scholar
  64. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O'Brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G (2006) microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci USA 103:9136–9141PubMedCrossRefGoogle Scholar
  65. Zhang JD, Biczok R, Ruschhaupt M (2011) The ddCt algorithm for the analysis of quantitative real-time PCR (qRT-PCR). Bioconductor 2.11 http://bioconductor.org/packages/release/bioc/html/ddCt.html
  66. Zhang Z, Sun H, Dai H, Walsh RM, Imakura M, Schelter J, Burchard J, Dai X, Chang AN, Diaz RL, Marszalek JR, Bartz SR, Carleton M, Cleary MA, Linsley PS, Grandori C (2009) MicroRNA miR-210 modulates cellular response to hypoxia through the MYC antagonist MNT. Cell Cycle 8:2756–2768PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Michael Sand
    • 1
    • 4
    Email author
  • Marina Skrygan
    • 1
  • Daniel Sand
    • 2
  • Dimitrios Georgas
    • 1
  • Thilo Gambichler
    • 1
  • Stephan A. Hahn
    • 3
  • Peter Altmeyer
    • 1
  • Falk G. Bechara
    • 1
  1. 1.Department of Dermatology, Venereology and AllergologyRuhr University BochumBochumGermany
  2. 2.Department of Medicine, Olive View UCLA Medical CenterUniversity of California, Los Angeles (UCLA)Los AngelesUSA
  3. 3.Department of Internal MedicineKnappschaftskrankenhaus University of Bochum, Zentrum für Klinische Forschung, Labor für Molekulare Gastroenterologische OnkologieBochumGermany
  4. 4.Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, St. Josef HospitalRuhr University BochumBochumGermany

Personalised recommendations