Mining the epigenome for methylated genes in lung cancer

Lung cancer has become a global public health burden, further substantiating the need for early diagnosis and more effective targeted therapies. The key to accomplishing both these goals is a better understanding of the genes and pathways disrupted during the initiation and progression of this disease. Gene promoter hypermethylation is an epigenetic modification of DNA at promoter CpG islands that together with changes in histone structure culminates in loss of transcription. The fact that gene promoter hypermethylation is a major mechanism for silencing genes in lung cancer has stimulated the development of screening approaches to identify additional genes and pathways that are disrupted within the epigenome. Some of these approaches include restriction landmark scanning, methylation CpG island amplification coupled with representational difference analysis, and transcriptome-wide screening. Genes identified by these approaches, their function, and prevalence in lung cancer are described. Recently, we used global screening approaches to interrogate 43 genes in and around the candidate lung cancer susceptibility locus, 6q23-25. Five genes, TCF21, SYNE1, AKAP12, IL20RA, and ACAT2, were methylated at 14 to 81% prevalence, but methylation was not associated with age at diagnosis or stage of lung cancer. These candidate tumor suppressor genes likely play key roles in contributing to sporadic lung cancer. The realization that methylation is a dominant mechanism in lung cancer etiology and its reversibility by pharmacologic agents has led to the initiation of translational studies to develop biomarkers in sputum for early detection and the testing of demethylating and histone deacetylation inhibitors for treatment of lung cancer.