A pilot study of DNA methylation in pediatric germ cell tumors

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DESCRIPTION (provided by applicant): Pediatric germ cell tumors (GCTs) are a heterogeneous group of tumors that are hypothesized to occur as a result of events in utero, although the etiology remains largely unknown. Aberrant DNA methylation, which has been implicated in the etiology of multiple types of cancer, has the potential to be especially relevant in GCTs due to the extensive epigenetic reprogramming that occurs in the germ line and early embryo during normal development. Limited evidence exists to support a potential role of epigenetic alterations in the development of GCTs; however, a comprehensive study of alterations in methylation patterns in pediatric GCTs has not been conducted to date. Our long term objective is to understand the role of epigenetic alterations in pediatric GCTs and how these alterations may be influenced by environmental exposures, with the goal of establishing a large genetic epidemiology study of pediatric GCT in the Children's Oncology Group. The primary objective for this pilot is to identify a panel of genes with altered promoter hypermethylation in DNA extracted from 58 pediatric GCTs, including germinomas, yolk sac tumors, teratomas and mixed germ cell tumors, overall and by histologic type. Our hypothesis is that DNA methylation in genes previously implicated in carcinogenesis will differ between tumor and normal tissue and also by tumor histology. To explore this hypothesis, the following specific aims will be evaluated: 1) identify genes with altered promoter hypermethylation in pediatric GCTs and 2) explore inter- and intratumoral heterogeneity in DNA methylation by tumor histology. We will evaluate DNA methylation using a two-staged approach. First, we will measure DNA methylation in a panel of 807 genes previously implicated in carcinogenesis using the Illumina GoldenGate Methylation Cancer Panel, which will allow us to select CpG sites that are characteristic of GCTs. We will then validate and expand the top15 CpG sites by Pyrosequencing on the same samples. At the completion of the proposed studies, it is our expectation that we will have identified a panel of genes with altered DNA methylation that are likely to be relevant in the development of pediatric GCT, and that these data will be included as preliminary data in an NIH R01 application to collect additional tumor and epidemiologic data for a study of the epigenetics of pediatric GCT. The research proposed in this application is significant because it will provide a more comprehensive understanding of DNA methylation in pediatric GCT in cancer-related genes throughout the genome as well as in tumors of different histologic subtypes. PUBLIC HEALTH RELEVANCE: Environmental exposures during fetal development and early life are thought to play a role in the development of cancer in both children and adults, although the mechanism by which these exposures influence disease risk is not clear. Extensive epigenetic reprogramming occurs immediately after fertilization (in the germ cells), and these epigenetic modifications are generally stable throughout the lifetime of mitotic cell divisions. A better understanding of these epigenetic changes may provide some insights on how early-life exposures lead to long-term alterations in gene function, and may provide important insights into the fetal origins of carcinogenesis. The overall objective of this pilot grant is to evaluate epigenetic alterations in pediatric germ cell tumors, which will be used as pilot data for a future epidemiologic study of this important and under- investigated cancer.