Complete and tissue-independent methylation of CpG sites in the p53 gene: implications for mutations in human cancers

Abstract

CpG dinucleotides are the target of about one third of transition mutations found in human genetic diseases and tumors. Methylation at these sites is thought to be the cause of these genetic changes through spontaneous deamination of 5-methylcytosine. In order to define the contribution of 5-methylcytosine to the spectrum of p53 mutations in human cancers, we have determined the complete DNA methylation pattern along exons 5-8 of the human p53 gene by ligation-mediated polymerase chain reaction genomic sequencing. The study was conducted with nine different types of normal human tissue and cell lines, including skin fibroblasts, keratinocytes, lung epithelial cells, mammary epithelial cells and colonic mucosa cells. We found that the p53 sequences along exons 5-8 are completely methylated at every CpG site, including 46 different sites on both DNA strands. This methylation pattern is tissue-independent suggesting that tissue-specific methylation does not contribute to the differential mutation patterns seen in tumors. The occurrence of mutational hotspots at specific CpG sites is not related to selective methylation of only a subset of CpGs but may rather depend on a selection bias for particular amino acid changes. Our results are not inconsistent with theories that mutations in tumors with high CpG mutation rates, like colon cancer, are caused by spontaneous deamination of 5-methylcytosine and mutations in tumors with a lack of CpG involvement reflect superimposed fingerprints from exogenous carcinogens. However, given the lack of tissue specificity of methylation, alternative explanations (eg targeting of methylated CpG sites by tissue-selective carcinogens) should be considered to explain the high percentage of CpG mutations in some tumor types.