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. 2003 Jun;4(3):329–336. doi: 10.1002/cfg.295

Methylation Analysis of Several Tumour Suppressor Genes Shows a Low Frequency of Methylation of CDKN2A and RARB in Uveal Melanomas

Michael Zeschnigk 1,✉, Frank Tschentscher 1, Christina Lich 1, Birgit Brandt 1, Bernhard Horsthemke 1, Dietmar R Lohmann 1
PMCID: PMC2448448  PMID: 18629284

Abstract

We have investigated the frequency of methylation of several tumour suppressor genes in uveal melanoma. As the loss of one copy of chromosome 3 (monosomy 3), which is found in about half of these tumours, is tightly associated with metastatic disease, a special emphasis was laid on genes located on this chromosome, including the fragile histidine triad (FHIT), von Hippel–Lindau (VHL), β-catenin (CTNNB1), activated leukocyte cell adhesion molecule (ALCAM) and retinoic acid receptor-β2 (RARB) genes. In addition, the methylation patterns of the CpG-rich regions 5′ of the E-cadherin (CDH1), p16/cyclin-dependent kinase inhibitor 2 A (CDKN2A) and retinoblastoma (RB1) genes were analysed by bisulphite genomic sequencing or methylation-specific PCR (MSP). Furthermore, the SNRPN and D15S63 loci, which are located in the imprinted region of chromosome 15, were included in the study. Aberrant methylation was detected in nine of 40 tumours analysed: The imprinted SNRPN and D15S63 loci were hypermethylated in three tumours, all of which retained both copies of chromosome 3. Methylated RARB alleles were detected in three tumours, whereas in three other tumours CDKN2A was found to be methylated. As we did not find RARB and CDKN2A preferentially methylated in tumours with monosomy 3, which is a significant predictor of metastatic disease, we suggest that these genes may play a causative role in the formation of uveal melanoma but not in the development of metastases.

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Selected References

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  1. Baylin S. B., Esteller M., Rountree M. R., Bachman K. E., Schuebel K., Herman J. G. Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet. 2001 Apr;10(7):687–692. doi: 10.1093/hmg/10.7.687. [DOI] [PubMed] [Google Scholar]
  2. Clark S. J., Harrison J., Paul C. L., Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994 Aug 11;22(15):2990–2997. doi: 10.1093/nar/22.15.2990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Dittrich B., Buiting K., Gross S., Horsthemke B. Characterization of a methylation imprint in the Prader-Willi syndrome chromosome region. Hum Mol Genet. 1993 Dec;2(12):1995–1999. doi: 10.1093/hmg/2.12.1995. [DOI] [PubMed] [Google Scholar]
  4. Greger V., Passarge E., Höpping W., Messmer E., Horsthemke B. Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma. Hum Genet. 1989 Sep;83(2):155–158. doi: 10.1007/BF00286709. [DOI] [PubMed] [Google Scholar]
  5. Herman J. G., Graff J. R., Myöhänen S., Nelkin B. D., Baylin S. B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9821–9826. doi: 10.1073/pnas.93.18.9821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Houle B., Rochette-Egly C., Bradley W. E. Tumor-suppressive effect of the retinoic acid receptor beta in human epidermoid lung cancer cells. Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):985–989. doi: 10.1073/pnas.90.3.985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Klutz M., Horsthemke B., Lohmann D. R. RB1 gene mutations in peripheral blood DNA of patients with isolated unilateral retinoblastoma. Am J Hum Genet. 1999 Feb;64(2):667–668. doi: 10.1086/302254. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Liu Y., Lee M. O., Wang H. G., Li Y., Hashimoto Y., Klaus M., Reed J. C., Zhang X. Retinoic acid receptor beta mediates the growth-inhibitory effect of retinoic acid by promoting apoptosis in human breast cancer cells. Mol Cell Biol. 1996 Mar;16(3):1138–1149. doi: 10.1128/mcb.16.3.1138. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Merbs S. L., Sidransky D. Analysis of p16 (CDKN2/MTS-1/INK4A) alterations in primary sporadic uveal melanoma. Invest Ophthalmol Vis Sci. 1999 Mar;40(3):779–783. [PubMed] [Google Scholar]
  10. Prescher G., Bornfeld N., Hirche H., Horsthemke B., Jöckel K. H., Becher R. Prognostic implications of monosomy 3 in uveal melanoma. Lancet. 1996 May 4;347(9010):1222–1225. doi: 10.1016/s0140-6736(96)90736-9. [DOI] [PubMed] [Google Scholar]
  11. Runte M., Färber C., Lich C., Zeschnigk M., Buchholz T., Smith A., Van Maldergem L., Bürger J., Muscatelli F., Gillessen-Kaesbach G. Comprehensive methylation analysis in typical and atypical PWS and AS patients with normal biparental chromosomes 15. Eur J Hum Genet. 2001 Jul;9(7):519–526. doi: 10.1038/sj.ejhg.5200661. [DOI] [PubMed] [Google Scholar]
  12. Sakai T., Toguchida J., Ohtani N., Yandell D. W., Rapaport J. M., Dryja T. P. Allele-specific hypermethylation of the retinoblastoma tumor-suppressor gene. Am J Hum Genet. 1991 May;48(5):880–888. [PMC free article] [PubMed] [Google Scholar]
  13. Scholes A. G., Liloglou T., Maloney P., Hagan S., Nunn J., Hiscott P., Damato B. E., Grierson I., Field J. K. Loss of heterozygosity on chromosomes 3, 9, 13, and 17, including the retinoblastoma locus, in uveal melanoma. Invest Ophthalmol Vis Sci. 2001 Oct;42(11):2472–2477. [PubMed] [Google Scholar]
  14. Sisley K., Rennie I. G., Parsons M. A., Jacques R., Hammond D. W., Bell S. M., Potter A. M., Rees R. C. Abnormalities of chromosomes 3 and 8 in posterior uveal melanoma correlate with prognosis. Genes Chromosomes Cancer. 1997 May;19(1):22–28. doi: 10.1002/(sici)1098-2264(199705)19:1<22::aid-gcc4>3.0.co;2-2. [DOI] [PubMed] [Google Scholar]
  15. Tschentscher F., Prescher G., Horsman D. E., White V. A., Rieder H., Anastassiou G., Schilling H., Bornfeld N., Bartz-Schmidt K. U., Horsthemke B. Partial deletions of the long and short arm of chromosome 3 point to two tumor suppressor genes in uveal melanoma. Cancer Res. 2001 Apr 15;61(8):3439–3442. [PubMed] [Google Scholar]
  16. Tschentscher F., Prescher G., Zeschnigk M., Horsthemke B., Lohmann D. R. Identification of chromosomes 3, 6, and 8 aberrations in uveal melanoma by microsatellite analysis in comparison to comparative genomic hybridization. Cancer Genet Cytogenet. 2000 Oct 1;122(1):13–17. doi: 10.1016/s0165-4608(00)00266-1. [DOI] [PubMed] [Google Scholar]
  17. White V. A., Chambers J. D., Courtright P. D., Chang W. Y., Horsman D. E. Correlation of cytogenetic abnormalities with the outcome of patients with uveal melanoma. Cancer. 1998 Jul 15;83(2):354–359. [PubMed] [Google Scholar]
  18. White V. A., McNeil B. K., Horsman D. E. Acquired homozygosity (isodisomy) of chromosome 3 in uveal melanoma. Cancer Genet Cytogenet. 1998 Apr 1;102(1):40–45. doi: 10.1016/s0165-4608(97)00290-2. [DOI] [PubMed] [Google Scholar]
  19. Widschwendter M., Berger J., Hermann M., Müller H. M., Amberger A., Zeschnigk M., Widschwendter A., Abendstein B., Zeimet A. G., Daxenbichler G. Methylation and silencing of the retinoic acid receptor-beta2 gene in breast cancer. J Natl Cancer Inst. 2000 May 17;92(10):826–832. doi: 10.1093/jnci/92.10.826. [DOI] [PubMed] [Google Scholar]
  20. Yap A. S. The morphogenetic role of cadherin cell adhesion molecules in human cancer: a thematic review. Cancer Invest. 1998;16(4):252–261. doi: 10.3109/07357909809039774. [DOI] [PubMed] [Google Scholar]
  21. Zeschnigk M., Lich C., Buiting K., Doerfler W., Horsthemke B. A single-tube PCR test for the diagnosis of Angelman and Prader-Willi syndrome based on allelic methylation differences at the SNRPN locus. Eur J Hum Genet. 1997 Mar-Apr;5(2):94–98. [PubMed] [Google Scholar]
  22. Zeschnigk M., Lohmann D., Horsthemke B. A PCR test for the detection of hypermethylated alleles at the retinoblastoma locus. J Med Genet. 1999 Oct;36(10):793–794. doi: 10.1136/jmg.36.10.793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Zöchbauer-Müller S., Fong K. M., Virmani A. K., Geradts J., Gazdar A. F., Minna J. D. Aberrant promoter methylation of multiple genes in non-small cell lung cancers. Cancer Res. 2001 Jan 1;61(1):249–255. [PubMed] [Google Scholar]
  24. van der Velden P. A., Metzelaar-Blok J. A., Bergman W., Monique H., Hurks H., Frants R. R., Gruis N. A., Jager M. J. Promoter hypermethylation: a common cause of reduced p16(INK4a) expression in uveal melanoma. Cancer Res. 2001 Jul 1;61(13):5303–5306. [PubMed] [Google Scholar]

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