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(PQD4) Epigenetic loss of heterozygosity as a driver of the cancer field effect

Alexander Gimelbrant

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National Institutes of Health (NIH)
Epigenetic loss of heterozygosity (eLOH) is a common process in normal human and mouse development, above and beyond the well-known example of X chromosome inactivation. Recent work has shown that eLOH is much more common than previously appreciated: over 10% of autosomal genes in human and mouse are subject to monoallelic silencing in a way that resembles X-inactivation. As a result of eLOH, even cells of the same type in the same individual can have dramatically different fates. When a tumor suppressing gene is affected, cells with the epigenetic silencing of the "good" allele give rise to tumors, while the cells with the opposite allelic choice remain normal. In fact, eLOH affects many cancer-related autosomal genes. Monoallelic silencing of the affected genes is mitotically stable and leads to formation of a mosaic in tissue, with cells in each patch sharing aparticular genome-wide eLOH pattern. We hypothesize that some eLOH patterns predispose cells to tumor initiation by causing functional LOH in critical genes. The cancer field effect woul be explained in this case by sharing the offensive eLOH pattern within clonal cell patches, while cells in neighboring patches would be tumor resistant because they carried harmless patterns. This project combines the unique expertise of two leading laboratories in breast cancer modeling and in genome-wide eLOH analysis. We will systematically explore and characterize the role of epigenetic LOH in the cancer field effect by combining our pioneering approaches to epigenomics of eLOH and expertise in mouse models of mammary tumor development. Using deep sequencing of RNA and chromatin, we will map genome- wide eLOH patterns in multifocal mammary tumors and compare them to such patterns in purified normal duct epithelial cells. If successful, the proposed work will establish a new conceptual framework for understanding the cancer field effect in the context of clonal lineages formed during normal development and differentiation. We will also have created a robust experimental platform for systematic study of the widespread phenomenon of epigenetic LOH. We believe this will have a major impact on our understanding of the epigenetic mechanisms underlying the cancer field effect. Since epigenetic processes are in principle reversible, our findings should suggest new strategies in cancer treatment and prevention using epigenetic modifiers.

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