Aberrant CpG-island methylation has non-random and tumour-type–specific patterns

Abstract

CpG islands frequently contain gene promoters or exons1 and are usually unmethylated in normal cells1,2,3. Methylation of CpG islands is associated with delayed replication, condensed chromatin and inhibition of transcription initiation4,5,6,7. The investigation of aberrant CpG-island methylation in human cancer has primarily taken a candidate gene approach, and has focused on less than 15 of the estimated 45,000 CpG islands8 in the genome. Here we report a global analysis of the methylation status of 1,184 unselected CpG islands in each of 98 primary human tumours using restriction landmark genomic scanning9 (RLGS). We estimate that an average of 600 CpG islands (range of 0 to 4,500) of the 45,000 in the genome were aberrantly methylated in the tumours, including early stage tumours. We identified patterns of CpG-island methylation that were shared within each tumour type, together with patterns and targets that displayed distinct tumour-type specificity. The expression of many of these genes was reactivated by experimental demethylation in cultured tumour cells. Thus, the methylation of particular subsets of CpG islands may have consequences for specific tumour types.

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Figure 1: Methylation detection in RLGS profiles.
Figure 2: Loss of NotI fragments from RLGS profiles is due to methylation.
Figure 3: Heterogeneity in CpG-island methylation across tumours.
Figure 4: Subsets of CpG islands are preferentially methylated.
Figure 5: Frequencies of aberrant CpG-island methylation of shared and tumour-type–specific targets.

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Acknowledgements

We thank M.S. Berger, A. Asai, A. Tamura and N. Shitara for glioma samples; S. Edge and E. Repasky for help in obtaining primary breast tumour tissue; R. Lothe for testicular tumours, T. Weber and M.A. Rodriguez-Bigas for colon tumour samples; B. Chadwick and J. Weger for nucleotide sequencing; B. Yuan for the automated sequence analysis; J. Eisel, A. Morrow, J. Popovich and Y.-Z. Wu for technical assistance; C. DeSmet for helpful discussions; and Y. Hayashizaki and the late V. Chapman for advice and encouragement. We thank the Cooperative Human Tissue Network (CHTN) Midwestern Division and the CALGB Leukemia Tissue Bank for providing tissue samples. This work was supported in part by the National Cancer Institute grant P30 CA16058 and CA80912 (to C.P.), the Coleman Leukemia Research Foundation grant 3U10CA31946-17S3, the Children's Hospital Research Foundation grant 216398, the Ladies Auxiliary of the Veterans of Foreign Wars grant 216498 and the Roswell Park Alliance Foundation. D.J.S. was supported by the Corixa Corporation and the T32 CA09338-20 Oncology Training Grant from the National Cancer Institute. M.C.F. was supported by a fellowship of the Dr. Mildred Scheel Stiftung für Krebsforschung/Deutsche Krebshilfe. J.F.C. was supported sequentially by the Basic Science Fellowship from the American Association for Cancer Research and by the Frances Goodrich and Albert Hackett Postdoctoral Fellowship from the American Brain Tumor Association.

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Correspondence to Joseph F. Costello or Christoph Plass.

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Costello, J., Frühwald, M., Smiraglia, D. et al. Aberrant CpG-island methylation has non-random and tumour-type–specific patterns. Nat Genet 24, 132–138 (2000) doi:10.1038/72785

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