Quantitative Analysis of DNA Methylation Profiles in Lung Cancer Identifies Aberrant DNA Methylation of Specific Genes and Its Association with Gender and Cancer Risk Factors

Abstract

The global increase in lung cancer burden, together with its poor survival and resistance to classical chemotherapy, underscores the need for identification of critical molecular events involved in lung carcinogenesis. Here, we have applied quantitative profiling of DNA methylation states in a panel of five cancer-associated genes (CDH1, CDKN2A, GSTP1, MTHFR , and RASSF1A) to a large case-control study of lung cancer. Our analyses revealed a high frequency of aberrant hypermethylation of MTHFR, RASSF1A, and CDKN2A in lung tumors as compared with control blood samples, whereas no significant increase in methylation levels of GSTP1 and CDH1 was observed, consistent with the notion that aberrant DNA methylation occurs in a tumor-specific and gene-specific manner. Importantly, we found that tobacco smoking, sex, and alcohol intake had a strong influence on the methylation levels of distinct genes (RASSF1A and MTHFR), whereas folate intake, age, and histologic subtype had no significant influence on methylation states. We observed a strong association between MTHFR hypermethylation in lung cancer and tobacco smoking, whereas methylation levels of CDH1, CDKN2A, GSTP1, and RASSF1A were not associated with smoking, indicating that tobacco smoke targets specific genes for hypermethylation. We also found that methylation levels in RASSF1A, but not the other genes under study, were influenced by sex, with males showing higher levels of methylation. Together, this study identifies aberrant DNA methylation patterns in lung cancer and thus exemplifies the mechanism by which environmental factors may interact with key genes involved in tumor suppression and contribute to lung cancer.

Quantitative promoter hypermethylation analysis of RASSF1A in lung cancer: Comparison with methylation-specific PCR technique and clinical significance

“…In the present study, RASSF1A methylation was discovered in 44.7 and 37.4% of the tumors by PS and MSP assays, respectively, being consistent with the previous data that RASSF1A methylation is typically observed in 30-40% of NSCLCs (12)(13)(14)(15). Moreover, regardless of the detection methods, RASSF1A methylation was more frequent in ever-smokers and TP53 mutation-positive tumors than in never-smokers and TP53 mutation-negative tumors, respectively.…”

“…To date, the prevalence of RASSF1A methylation is exhibited in 30-40% of non-small cell lung cancers (NSCLCs), which have mainly been determined by MSP analysis (12). However, only one study of methylation status by PS analysis has been performed in NSCLCs (15). Furthermore, there is no report to compare RASSF1A methylation status in NSCLCs by qualitative MSP and quantitative PS methods, and correlate their results with survival outcomes of patients with NSCLC.…”

Modeling DNA methylation by analyzing the individual configurations of single molecules

“…[2][3][4][5][6][7][8] Such an approach provides important information on the general relationships between methylation and expression, but it does not look at the specific molecules conformation in each cell. As a consequence, it cannot accurately describe the complex epigenetic structure within a cell population.…”

Genetic and epigenetic changes in lung carcinoma and their clinical implications

“…In lung adenocarcinomas/squamous cell carcinomas, the frequency of p16, MGMT, RASSF1, MTHFR, and FHIT promoter methylation was significantly higher among smokers than never-smokers. [98][99][100][101] On the other hand, methylation in certain genes, such as RASSF2, TNFRSF10C, BHLHB5, and BOLL, 102,103 was higher in lung cancers from never-smokers than those from smokers, suggesting smoking may target specific genes for methylation.…”