Purpose: Epigenetic gene silencing plays important roles in cancer initiation and progression. The aim of the current study was to investigate the prognostic value of DNA hypermethylation in patients with non-small cell lung cancer (NSCLC). Experimental Design: We examined the methylation status of a panel of 9 genes p16, RAS association domain family 1A (RASSF1A), E-cadherin (CDH1), tissue inhibitor of metalloproteinase-3 (TIMP3), adenomatous polyposis coli (APC), death-associated protein kinase (DAPK), fragile histidine triad (FHIT), O6-methylguanine-DNA-methyltransferase (MGMT), glutathione S-transferase P1 (GSTP1) using quantitative real-time methylation-specific PCR in 155 tumors from patients with NSCLC. We analyzed the associations between gene methylation status and patient survival. Results: Among 155 patients with NSCLC (56.1% stage I, 20.0% stage II, 25.9% stage III), the median survival time was 29.6 months and the 5-year survival rate was 54.8%. Methylation frequencies of the genes analyzed were 21.9% for p16, 27.1% for RASSF1A, 47.1% for TIMP-3, 32.9% for CDH1, 67.1% for APC, 53.5% for DAPK, 31.6% for FHIT, 17.4% for MGMT, and 5.8% for GSTP1. In the Cox proportional hazards model, hypermethylation of p16 was associated with a significantly poorer survival (HR=1.95, 95% CI=1.12-3.39) and the association was more evident in squamous carcinoma than in adenocarcinoma, and in older patients than in younger patients. Kaplan-Meier survival curves showed that patients with hypermethylated p16 had significantly shorter survival (median = 21.7 months) than patients without p16 hypermethylation (median = 62.5 months, p = 0.0001, log-rank test). Hypermethylation of CDH1 and TIMP3 were associated with significantly better survival with HRs of 0.51 (95% CI=0.29-0.90) and 0.59 (95% CI=0.36-0.97), respectively. Patients with hypermethylated CDH1 or TIMP3 exhibited significantly longer survival than those without hypermethylation (p= 0.0002 and 0.01, respectively). Joint analysis of these three genes showed a significant trend for poorer survival as the number of unfavorable methylation status increased (P for trend = 0.002). Conclusions: Hypermethylation of multiple genes exhibited significant differential impact on NSCLC patient survival. The individual gene methylation and the combination of multiple gene methylations may become valuable prognostic markers of clinical outcome of NSCLC patients. Supported by NCI CA 55769, CA 111646, CA 70907, DAMD17-02-1-0706 and Flight Attendant Medical Research Institute.

[Proc Amer Assoc Cancer Res, Volume 47, 2006]