Lee Moore

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NCI, DCEG, OEEB

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PLCO (Learn more about this study)

2013-0033

Mar 4, 2013

Genome wide epigenetic alteration study to identify biomarkers of smoking and bladder cancer risk

Environmental and genetic factors play an important role in cancer etiology and development, however the epigenetic component of cancer risk is largely unexplored. Recent published and unpublished data by our group and others indicate that epigenetic traits observed in white blood cell DNA are good candidate risk markers for solid tumors. We propose to conduct a multi-stage genome-wide blood DNA methylation study to identify makers of bladder cancer risk, on a total of 2,000 cases and 2,000 controls from three prospective cohort studies (PLCO, ATBC and EPIC). In stage I, we will run the Illumina 450K Infinium array designed to cover both promoter and gene-body sequences, on 500 cases and 500 controls nested in the PLCO cohort. In a stage II study of 1,500 cases and 1,500 controls from ATBC and EPIC, potential risk markers identified will be followed up using a custom Illumina array with 10,000 probes In stage III, candidate gene loci will be further validated using bisulphite pyrosequencing. This stage will assess platform variation, and provide pyrosequencing validation on a subset of 200 cases and 200 controls from PLCO. We also plan to use these data to identify life-style, environmental (e.g. smoking, dietary) and genetic determinants of DNA methylation in the combined sample set of 2,000 cases and 2,000 controls analysed in stages I+II. For the stage I phase, we are requesting 500 superficial and muscle invasive bladder cancer cases and 500 controls from PLCO with consent, baseline questionnaire and pre-diagnostic blood DNA samples. To our knowledge, this will be the first large-scale, genome-wide methylation study of bladder cancer risk. At the conclusion of the project, we expect to identify novel exposure and risk that will improve our understanding of the epigenetic element in the etiology of bladder cancer.

Our central hypothesis is that white blood cell (WBC) DNA methylation levels can serve as risk biomarkers for bladder cancer development. This hypothesis is based on data from our group showing that global methylation in WBC DNA as measured by LINE1 is associated with bladder cancer risk in the PLCO and ATBC cohorts Thus, this proposal is designed to follow-up and extend upon our previous work in PLCO.

Aim 1: To identify and characterize methylation markers of bladder cancer risk using pre-diagnostically collected WBC DNA and a genome-wide methylation array (>450,000 CpG sites). We will propose to use a multi-stage genome-wide approach consisting of a nested cancer case-control design among participants in the PLCO Trial in the first stage and follow-up in additional cohort studies (ATBC, EPIC).

Aim 2: To identify environmental and genetic determinants of DNA methylation in PLCO using well-characterized subjects with respect to smoking habits, global LINE1 methylation levels, nutritional intake of micronutrients involved in DNA methylation and genetic susceptibility data. We will also evaluate relationships between tobacco exposure, methylation biomarkers identified in Aim 2 and future bladder cancer risk using data from PLCO and replication cohorts.