Changes in DNA methylation patterns are an important characteristic of human
cancer including
lung cancer. In particular, hypermethylation of CpG islands is a signature of malignant progression. Methylated CpG islands are promising diagnostic markers for the early detection of
cancer. However, the full extent and sequence context of
DNA hypermethylation in
lung cancer has remained unknown. We have used the methylated CpG island recovery assay and high-resolution microarray analysis to find hypermethylated CpG islands in
squamous cell carcinomas (SCC) and
adenocarcinomas of the lung. Each
tumor contained several hundred hypermethylated CpG islands. In an initial microarray screen, 36 CpG islands were methylated in five of five (=100%) of the SCC
tumors tested and 52 CpG islands were methylated in at least 75% of the
adenocarcinomas tested (n=8). Using
sodium-bisulfite-based approaches, 12 CpG islands (associated with the BARHL2, EVX2, IRX2, MEIS1, MSX1, NR2E1, OC2, OSR1, OTX1, PAX6, TFAP2A, and ZNF577 genes) were confirmed to be methylated in 85% to 100% of the
squamous cell carcinomas and 11 CpG islands (associated with the CHAD, DLX4, GRIK2, KCNG3, NR2E1, OSR1, OTX1, OTX2, PROX1, RUNX1, and VAX1 genes) were methylated in >80% of the
adenocarcinomas. From the list of genes that were methylated in
lung adenocarcinomas, we identified the gene FAT4 and found that this gene was methylated in 39% of the
tumors. FAT4 is the closest mammalian homologue of the Drosophila
tumor suppressor Fat which is an important component of the Hippo growth control pathway. Many of these newly discovered methylated CpG islands hold promise for becoming
biomarkers for the early detection of
lung cancer.