Global methylation profiling of lung cancer identifies novel methylated genes

Epigenetic changes, including DNA methylation, are a common finding in canc er. In lung cancers methylation of cytosine residues may affect tumor initi ation and progression in several ways, including the silencing of tumor sup pressor genes through promoter methylation and by providing the targets for adduct formation of polycyclic aromatic hydrocarbons present in combustion products of cigarette smoke. Although the importance of aberrant DNA methy lation is well established, the extent of DNA methylation in lung cancers h as never been determined. Restriction landmark genomic scanning (RLGS) is a highly reproducible two-dimensional gel electrophoresis that allows the de termination of the methylation status of up to 2000 promoter sequences in a single gel. We selected 1184 CpG islands for RLGS analysis and determined their methylation status in 16 primary non-small cell lung cancers. Some tu mors did not show methylation whereas others showed up to 5.3% methylation in all CpG islands of the profile. Cloning of 21 methylated loci identified 11 genes and 6 ESTs. We demonstrate that methylation is part of the silenc ing process of BMP3B in primary tumors and lung cancer cell lines.