Studies in this competitive renewal will test the hypothesis that the propensity for silencing of tumor suppressor genes in the respiratory epithelium of chronic smokers by promoter hypermethylation is influenced by sequence variations that modify the activity of genes and microRNAs that directly or indirectly influence de novo methylation and chromatin remodeling. This hypothesis will be tested through four specific aims.
Aim 1 will discover and validate gene sequence variations, copy number variants, and haplotypes that are determinants of gene promoter hypermethylation using a whole genome-wide association study (GWAS). A GWAS using the Illumina 610K BeadChip will be performed on 1,500 non-Hispanic white members of the Lovelace Smokers Cohort to identify SNPs significantly associated with extent of methylation of an 8-gene panel in sputum. SNPs across the genome;within microRNA coding and 3'untranslated regions of genes will be identified and validated for their association with methylation in 1,000 members of the PluSS Cohort from the Pittsburgh Lung SPORE and then assessed for association with lung cancer through multi-center case- control studies.
Aim 2 will focus on identifying sequence variation in the promoter region of precursor microRNAs and their target genes involved in cytosine methylation and histone modification and evaluate their association with gene methylation and lung cancer.
Aim 3 will translate findings from the population-based studies back to the laboratory bench to address how the identified gene haplotypes and SNPs associated with methylation in sputum affect the pathways in which they reside and influence the propensity for methylation.
Aim 4 will address whether integrating validated SNPs and haplotypes identified through GWAS and associated with methylation and lung cancer can improve the positive and negative predictive value of gene methylation detection in sputum for early lung cancer diagnosis. A nested, case-control study within ACRIN, a prospective cohort of people at high risk for cancer within the National Lung Screening Trial will be conducted through the Johns Hopkins and Colorado Lung SPOREs. Gene methylation assays in sputum will be conducted through our SPORE project with Johns Hopkins and genotyping of validated SNPs and haplotypes will be done through this grant. These studies are highly relevant to the mission of the NCI to reduce the suffering and health burden of cancer: they will uncover genes and microRNAs whose altered regulation due to inherited sequence variations are critical for the silencing of genes by promoter hypermethylation, a key-step in the development of lung cancer and likely an intermediate marker for risk. Therefore, these studies will identify biomarkers for risk assessment and early detection of lung cancer, the leading cause of cancer-related death in the U.S.

Public Health Relevance

Studies in this application could lead to the development of a comprehensive model using clinical risk factors, genetic variation, and gene methylation in sputum for early lung cancer detection.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
Project #
Application #
Study Section
Cancer Biomarkers Study Section (CBSS)
Program Officer
Kagan, Jacob
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Lovelace Biomedical & Environmental Research
United States
Zip Code
Bruse, Shannon; Petersen, Hans; Weissfeld, Joel et al. (2014) Increased methylation of lung cancer-associated genes in sputum DNA of former smokers with chronic mucous hypersecretion. Respir Res 15:2
Leng, Shuguang; Liu, Yushi; Thomas, Cynthia L et al. (2013) Native American ancestry affects the risk for gene methylation in the lungs of Hispanic smokers from New Mexico. Am J Respir Crit Care Med 188:1110-6
Schmiege, Sarah J; Meek, Paula; Bryan, Angela D et al. (2012) Latent variable mixture modeling: a flexible statistical approach for identifying and classifying heterogeneity. Nurs Res 61:204-12
Leng, Shuguang; Stidley, Christine A; Liu, Yushi et al. (2012) Genetic determinants for promoter hypermethylation in the lungs of smokers: a candidate gene-based study. Cancer Res 72:707-15
Leng, Shuguang; Bernauer, Amanda M; Hong, Chibo et al. (2011) The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premalignant lesions from smokers and in lung adenocarcinomas. Clin Cancer Res 17:2014-23
Machida, Emi Ota; Brock, Malcolm V; Hooker, Craig M et al. (2006) Hypermethylation of ASC/TMS1 is a sputum marker for late-stage lung cancer. Cancer Res 66:6210-8
Divine, Kevin K; Liechty, Kieu C; Crume, Kevin C et al. (2006) Nested multigene MSP/DHPLC method for analyzing promoter hypermethylation status in clinical samples. Biotechniques 40:40, 42, 44 passim
Belinsky, Steven A; Klinge, Donna M; Dekker, Joseph D et al. (2005) Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin Cancer Res 11:6505-11