A genome-wide search for acquired promoter methylation in human lung cancer

Abstract

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As part of a genome-wide screen for promoter regions that are methylated in human lung cancer, we compared the gene expression profiles (Affymetrix U133 Plus 2.0) of 7 non-small cell lung cancers (NSCLC) and 3 immortalized human bronchial epithelial cells (HBECs) before and after treatment with 5-aza-2′-deoxycytidine (5-aza, 100 nM and 1 μM). We identified 123 genes that were expressed in the untreated HBECs, induced >4 fold by 5-aza in several lung cancer lines, and also have promoter region CpG islands. We confirmed gene induction for 20 of the genes by quantitative PCR. We performed methylation specific PCR (MSP) on 45/123 of the genes in 39 NSCLC lines, 17 HBEC lines, normal lymphocytes, and a panel of 20 primary NSCLC tumors and matched normal lung samples. 31/45 gene promoters were methylated in the NSCLC lines and primary tumors, but not in normal lymphocytes, HBECs, and rarely in matched normal lung tissue. Methylation frequencies in primary tumors ranged from 10% –100%. We selected 20 loci that were subject to frequent, tumor specific methylation and were also deleted as determined by array CGH in our panel of NSCLC lines. DNA methylation at these loci was analyzed further in a broader panel of 70 NSCLC tumors and matched normal lung samples. Univariate and multivariate statistical approaches were used to compare differences in methylation between cancer and normal tissue, as well as between cancer cell lines and normal cell lines. We have found several novel loci that distinguish cancer from normal lung tissue with high sensitivity and specificity. These multiple new methylated DNA sequences provide new markers for early detection, prognosis, and epigenetic targeting studies, as well as genes to test for functional roles in lung cancer pathogenesis.