Brain Tumor Pathology

, Volume 17, Issue 2, pp 49–56 | Cite as

Aberrant methylation of genes in low-grade astrocytomas

  • Joseph F. Costello
  • Christoph Plass
  • Webster K. Cavenee
Original Article


The underlying basis of the malignant progression of astrocytomas is a specific and cumulative series of genetic alterations, most of which are confined to high-grade tumors. In contrast, a proportion of low-grade astrocytomas have a relatively normal-appearing genome when examined with standard genetic screening methods. These methods do not detect epigenetic events such as aberrant methylation of CpG island, which result in transcriptional silencing of important cancer genes. To determine if aberrant methylation is involved in the early stages of astrocytoma development, we assessed the methylation status of 1184 genes in each of 14 low-grade astrocytomas using restriction landmark genome scanning (RLGS). The results showed nonrandom and astrocytoma-specific patterns of aberrantly methylated genes. We estimate that an average of 1544 CpG island-associated genes (range, 38 to 3731) of the approximately 45,000 in the genome are aberrantly methylated in each tumor. Expression of a significant proportion of the genes could be reactivated by 5-aza-2-deoxycytidine-induced demethylation in cultured glioma cell lines. The data suggest that aberrant methylation of genes is more prevalent than genetic alterations and may have consequences for the development of low-grade astrocytomas.

Key words

Low-grade astrocytoma Methylation RLGS CpG island 


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  1. 1.
    Kleihues P, Ohgaki H (1999) Primary and secondary glioblastoma: from concept to clinical diagnosis. Neuro-Oncology 1:44–51PubMedCrossRefGoogle Scholar
  2. 2.
    Cavenee WK, Furnari FB, Nagane M et al. (2000) Diffusely infiltrating astrocytomas. In: Cavenee WK, Kleihues P (eds) Tumours of the nervous system. IARC Press, Lyon, pp 9–52Google Scholar
  3. 3.
    Baylin SB, Herman JG, Graff JR, et al. (1998) Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 72:141–196PubMedCrossRefGoogle Scholar
  4. 4.
    Jones PA, Laird PW (1999) Cancer epigenetics comes of age. Nature Gene 21:163–167CrossRefGoogle Scholar
  5. 5.
    Gama-Sosa MA, Slagel VA, Trewyn RW, et al. (1983) The 5-methylcytosine content of DNA from human tumors. Nucl Acids Res 11:6883–6894PubMedGoogle Scholar
  6. 6.
    Chen RZ, Pettersson U, Beard C et al. (1998) DNA hypomethylation leads to elevated mutation rates. Nature 395:89–93PubMedCrossRefGoogle Scholar
  7. 7.
    Stirzaker C, Millar DS, Paul CL et al. (1997) Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors. Cancer Res 57:2229–2237PubMedGoogle Scholar
  8. 8.
    Herman JG, Latif F, Weng, Y, et al. (1994) Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma. Proc Nat Acad Sci USA 91:9700–9704PubMedCrossRefGoogle Scholar
  9. 9.
    Kane MF, Loda M, Gaida GM, et al. (1997) Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res 57:808–811PubMedGoogle Scholar
  10. 10.
    Costello JF, Futscher BW, Kroes RA, et al. (1994) Methylation-related chromatin structure is associated with exclusion of transcription factors from and suppressed expression of the O-6-methylguanine DNA methyltransferase gene in human glioma cell lines. Mol Cell Bio 14:6515–6521Google Scholar
  11. 11.
    Li Q, Ahuja N, Burger PC, et al. (1999) Methylation and silencing of the thrombospondin-1 promoter in human cancer. Oncogene 18:3284–3289PubMedCrossRefGoogle Scholar
  12. 12.
    Graff JR, Herman JG, Lapidus RG, et al. (1995) E-cadherin expression is silenced by DNA hypermethylation in human breast and prostate carcinomas. Cancer Res 55:5195–5199PubMedGoogle Scholar
  13. 13.
    Antequera F, Bird A (1993) Number of CpG islands and genes in human and mouse. Proc Nat Acad USA 90:11995–11999CrossRefGoogle Scholar
  14. 14.
    Hatada I, Hayashizaki Y, Hirotsune S, et al. (1991) A genomic scanning method for higher organisms using restriction sites as landmarks. Proc Nat Acad Sci USA 88:9523–9527PubMedCrossRefGoogle Scholar
  15. 15.
    Lindsay S, Bird AP (1987) Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature 327:336–338PubMedCrossRefGoogle Scholar
  16. 16.
    Plass C, Shibata H, Kalcheva I, et al. (1996) Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M. Nature Genetics 14:106–109PubMedCrossRefGoogle Scholar
  17. 17.
    Hayashizaki Y, Shibata, H, Hirotsune S, et al. (1994) Identification of an imprinted U2af binding protein related sequence on mouse chromosome 11 using the RLGS method. Nature Genet 6:33–40PubMedCrossRefGoogle Scholar
  18. 18.
    Costello JF, Plass C, Arap W, et al. (1997) Cyclin-dependent kinase 6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA. Cancer Res 57:1250–1254PubMedGoogle Scholar
  19. 19.
    Frühwald MC, O'Dorisio MS, Rush L, et al. (2000) Gene amplification in PNET/medulloblastoma: mapping of a novel amplified gene within the MYCN amplicon. J Med Genet 37:501–509PubMedCrossRefGoogle Scholar
  20. 20.
    Costello JF, Fruhwald MC, Smiraglia DJ, et al. (2000) Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nature Genet 24:132–138PubMedCrossRefGoogle Scholar
  21. 21.
    Plass C, Yu F, Yu L, et al. (1999) Restriction landmark genome scanning for aberrant methylation in primary refractory and relapsed acute myeloid leukemia; involvement of the WIT-1 gene. Oncogene 18:3159–3165PubMedCrossRefGoogle Scholar
  22. 22.
    Akama TO, Okazaki Y, Ito M, et al. (1997) Restriction landmark genomic scanning (RLGS-M)-based genome-wide scanning of mouse liver tumors for alterations in DNA methylation status. Cancer Res 57:3294–3299PubMedGoogle Scholar
  23. 23.
    Yoshikawa H, de la Monte S, Nagai H, et al. (1996) Chromosomal assignment of human genomicNotI restriction fragments in a two-dimensional electrophoresis profile. Genomics 31:28–35PubMedCrossRefGoogle Scholar
  24. 24.
    Graff JR, Herman JG, Myöhänen S, et al. (1997) Mapping patterns of CpG island methylation in normal and neoplastic cells implicates both upstream and downstream regions in de novo methylation. J Biol Chem 272:22322–22329PubMedCrossRefGoogle Scholar
  25. 25.
    Graff JR, Greenberg VE, Herman JG, et al. (1998) Distinct patterns of E-cadherin CpG island methylation in papillary, follicular, Hurthle's cell, and poorly differentiated human thyroid carcinoma. Cancer Res 58:2063–2066PubMedGoogle Scholar
  26. 26.
    Plass C, Weichenhan D, Catanese J, et al. (1997) An arrayed humanNotI-EcoRV boundary library as a tool for RLGS spot analysis. DNA Res 4:253–255PubMedCrossRefGoogle Scholar
  27. 27.
    Smiraglia DJ, Frühwald MC, Costello JF, et al. (1999) A new tool for the rapid cloning of amplified and hypermethylated human DNA sequences from restriction landmark genomic scanning gels. Genomics 58:254–262PubMedCrossRefGoogle Scholar
  28. 28.
    Bachman KE, Herman JG, Corn PG, et al. (1999) Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggests a suppressor role in kidney, brain, and other human cancers. Cancer Res 59:798–802PubMedGoogle Scholar
  29. 29.
    Merlo A, Herman JG, Mao L et al. (1995) 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nature Med 1:686–692PubMedCrossRefGoogle Scholar
  30. 30.
    Myöhânen SK, Baylin SB, Herman JG (1998) Hypermethylation can selectively silence individual p16ink4A alleles in neoplasia. Cancer Res 58:591–593PubMedGoogle Scholar
  31. 31.
    Nan X, Tate P, Li E, et al. (1996) DNA methylation specifies chromosomal localization of MeCP2. Mol Cell Biol 16:414–421PubMedGoogle Scholar
  32. 32.
    Cameron EE, Bachman KE, Myöhänen S, et al. (1999) Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nature Genet 21:103–107PubMedCrossRefGoogle Scholar
  33. 33.
    Bermingham JR Jr, Scherer SS, O'Connell S, et al. (1996) Tst-1/Oct-6/SCIP regulates a unique step in peripheral myelination and is required for normal respiration. Genes Dev 10:1751–1762PubMedGoogle Scholar
  34. 34.
    Nambu JR, Franks RG, Hu S, et al. (1990) The single-minded gene of Drosophila is required for the expression of genes important for the development of CNS midline cells. Cell 63:63–75PubMedCrossRefGoogle Scholar
  35. 35.
    Offermanns S, Simon MI (1996) Organization of transmembrane signalling by heterotrimeric G proteins. Cancer Surv 27:177–198PubMedGoogle Scholar
  36. 36.
    Kallioniemi A, Kallioniemi OP, Sudar D, et al. (1992) comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818–821PubMedGoogle Scholar
  37. 37.
    Cavenee WK, Dryja TP, Phillips RA, et al. (1983) Expression of recessive alleles by chromosomal mechanisms in retinoblastoma. Nature 305:779–784PubMedCrossRefGoogle Scholar
  38. 38.
    Mertens F, Johansson B, Höglund M, et al. (1997) Chromosomal imbalance maps of malignant solid tumors: a cytogenetic survey of 3185 neoplasms. Cancer Res 57:2765–2780PubMedGoogle Scholar
  39. 39.
    Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282PubMedCrossRefGoogle Scholar

Copyright information

© The Japan Society of Brain Tumor Pathology 2000

Authors and Affiliations

  • Joseph F. Costello
    • 1
  • Christoph Plass
    • 2
  • Webster K. Cavenee
    • 3
  1. 1.The Brain Tumor Research CenterUniversity of California-San FranciscoSan FranciscoUSA
  2. 2.Division of Human Cancer GeneticsThe Ohio State universityColumbusUSA
  3. 3.Ludwig Institute for Cancer Research, Department of Medicine and Center for Molecular GeneticsUniversity of California-San DiegoLa JollaUSA

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