Skip to main content
SpringerLink
Log in

Gene Expression Array Analysis to Identify Candidate Tumor Suppressor Genes in Melanoma

  • Protocol
  • First Online:
Methods in Molecular Biology

Part of the book series: Methods in Molecular Biology

  • 208 Accesses

Abstract

Melanoma is a complex multifactorial disease; therefore, a combination of various approaches is necessary to girt all aspects of its biology and identify the many different genes and factors involved in its etiology.

Epigenetic regulation of tumor suppressor genes (TSGs) has been shown to play a central role in melanomagenesis. Here, we describe a new pipeline based on an integrative and comparative analysis of several array platform, post-demethylation treatment expression data, methylation array, and constitutive mRNA expression analysis to identify novel TSGs frequently methylated in melanoma.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  1. Dutton-Regester K, Hayward NK (2012) Reviewing the somatic genetics of melanoma: from current to future analytical approaches. Pigment Cell Melanoma Res 25:144–154

    Article  CAS  PubMed  Google Scholar 

  2. Dutton-Regester K, Irwin D, Hunt P, Aoude LG, Tembe V et al (2012) A high-throughput panel for identifying clinically relevant mutation profiles in melanoma. Mol Cancer Ther 11:888–897

    Article  CAS  PubMed  Google Scholar 

  3. Perera RJ, Ray A (2012) Epigenetic regulation of miRNA genes and their role in human melanomas. Epigenomics 4:81–90

    Article  CAS  PubMed  Google Scholar 

  4. Glud M, Gniadecki R (2013) MicroRNAs in the pathogenesis of malignant melanoma. J Eur Acad Dermatol Venereol. 27(2):142–50. doi: 10.1111/j.1468-3083.2012.04579.x. Epub 2012 May 23

    Google Scholar 

  5. Bonazzi VF, Stark MS, Hayward NK (2012) MicroRNA regulation of melanoma progression. Melanoma Res 22:101–113

    Article  CAS  PubMed  Google Scholar 

  6. Castellano M, Pollock PM, Walters MK, Sparrow LE, Down LM et al (1997) CDKN2A/p16 is inactivated in most melanoma cell lines. Cancer Res 57:4868–4875

    CAS  PubMed  Google Scholar 

  7. Walker GJ, Flores JF, Glendening JM, Lin AH, Markl ID et al (1998) Virtually 100% of melanoma cell lines harbor alterations at the DNA level within CDKN2A, CDKN2B, or one of their downstream targets. Genes Chromosomes Cancer 22:157–163

    Article  CAS  PubMed  Google Scholar 

  8. Stark M, Hayward N (2007) Genome-wide loss of heterozygosity and copy number analysis in melanoma using high-density single-nucleotide polymorphism arrays. Cancer Res 67:2632–2642

    Article  CAS  PubMed  Google Scholar 

  9. Boyle GM, Woods SL, Bonazzi VF, Stark MS, Hacker E et al (2011) Melanoma cell invasiveness is regulated by miR-211 suppression of the BRN2 transcription factor. Pigment Cell Melanoma Res 24:525–537

    Article  CAS  PubMed  Google Scholar 

  10. Pavey S, Johansson P, Packer L, Taylor J, Stark M et al (2004) Microarray expression profiling in melanoma reveals a BRAF mutation signature. Oncogene 23:4060–4067

    Article  CAS  PubMed  Google Scholar 

  11. Bonazzi VF, Irwin D, Hayward NK (2009) Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma. Genes Chromosomes Cancer 48:10–21

    Article  CAS  PubMed  Google Scholar 

  12. Bonazzi VF, Nancarrow DJ, Stark MS, Moser RJ, Boyle GM et al (2011) Cross-platform array screening identifies COL1A2, THBS1, TNFRSF10D and UCHL1 as genes frequently silenced by methylation in melanoma. PLoS One 6:e26121

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  13. Weisenberger DJ Berg DVD, Pan F, Berman BP, Laird PW (2008) Comprehensive DNA methylation analysis on the Illumina Infinium assay platform. In: Illumina I (ed) http://wwwilluminacom/Documents/products/appnotes/appnote_infinium_methylationpdf. Technical Report, San Diego

    Google Scholar 

  14. Johansson P, Pavey S, Hayward N (2007) Confirmation of a BRAF mutation-associated gene expression signature in melanoma. Pigment Cell Res 20:216–221

    Article  CAS  PubMed  Google Scholar 

  15. Packer LM, Pavey SJ, Boyle GM, Stark MS, Ayub AL et al (2007) Gene expression profiling in melanoma identifies novel downstream effectors of p14ARF. Int J Cancer 121:784–790

    Article  CAS  PubMed  Google Scholar 

  16. Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ (2007) Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35:e119

    Article  PubMed  PubMed Central  Google Scholar 

  17. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T et al (2005) Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A 102:15785–15790

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  18. Leonard JH, Marks LH, Chen W, Cook AL, Boyle GM et al (2003) Screening of human primary melanocytes of defined melanocortin-1 receptor genotype: pigmentation marker, ultrastructural and UV-survival studies. Pigment Cell Res 16:198–207

    Article  CAS  PubMed  Google Scholar 

  19. Ehrich M, Zoll S, Sur S, van den Boom D (2007) A new method for accurate assessment of DNA quality after bisulfite treatment. Nucleic Acids Res 35:e29

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was funded through grants from the National Health and Medical Research Council of Australia (grant number 633004) and Cure Cancer Australia (grant number 552466). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author information

Authors and Affiliations

  1. Dermatology Research Centre, The University of Queensland, Woolloongabba, QLD, Australia

    Mitchell S. Stark

  2. Endometrial Cancer Laboratory, Translational Research Institute, Queensland University of Technology, 37 Kent Street, Woolloongabba, QLD, 4102, Australia

    Vanessa F. Bonazzi

Authors
  1. Mitchell S. Stark
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vanessa F. Bonazzi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vanessa F. Bonazzi .

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Stark, M.S., Bonazzi, V.F. (2017). Gene Expression Array Analysis to Identify Candidate Tumor Suppressor Genes in Melanoma. In: Methods in Molecular Biology. Humana Press. https://doi.org/10.1007/7651_2017_54

Download citation

  • DOI: https://doi.org/10.1007/7651_2017_54

  • Published:

  • Publisher Name: Humana Press

Publish with us

Policies and ethics

Search

Navigation