Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other, suggesting that these cDMRs might be generalized across cancer types. Here we show stochastic methylation variation of the same cDMRs, distinguishing cancer from normal tissue, in colon, lung, breast, thyroid and Wilms' tumors, with intermediate variation in adenomas. Whole-genome bisulfite sequencing shows these variable cDMRs are related to loss of sharply delimited methylation boundaries at CpG islands. Furthermore, we find hypomethylation of discrete blocks encompassing half the genome, with extreme gene expression variability. Genes associated with the cDMRs and large blocks are involved in mitosis and matrix remodeling, respectively. We suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer that may contribute to tumor heterogeneity.
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We thank C. Adams and Applied Biosystems, Inc. for supplying reagents for the sequencing experiments, B. Vogelstein, F. Giardiello and M. Zeiger for tumor samples and M. Newhouse for computer assistance. This work was supported by US National Institutes of Health grants R37CA054358, R01HG005220, 5P50HG003233, F32CA138111, 5R01GM083084 and R01DA025779 (K.Z.).
The authors declare no competing financial interests.
Supplementary Note, Supplementary Tables 1, 2, 4–6, 8–10 and 13–19 and Supplementary Figures 1–24. (PDF 15293 kb)
List of block locations (XLS 2912 kb)
List of small DMRs (XLS 1969 kb)
List of genes showing statistically significant over-expression in cancer compared to normal samples and are within 2,000 bp from an outward methylation boundary shift. (XLS 263 kb)
Genes with higher gene expression variability in cancer compared to normal. (XLS 170 kb)
Primers used for bisulfite pyrosequencing (XLS 35 kb)
List of microarrays used to identify tissue-specific genes (XLS 87 kb)
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Hansen, K., Timp, W., Bravo, H. et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43, 768–775 (2011). https://doi.org/10.1038/ng.865
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