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University of California-Berkeley

Superfund Research Program

Functional profiling of susceptibility genes

Project Leader: Christopher D. Vulpe
Co-Investigator: Luoping Zhang
Grant Number: P42ES004705
Funding Period: 2006-2017

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Project Summary (2006-2011)

Humans vary in their genetic susceptibility to the toxic effects of chemicals found at Superfund sites. Cancers and other forms of toxicity may arise from adverse gene-environment interactions. Genetic susceptibility to the toxic effects of a chemical is likely to be related to the cellular targets of the chemical and its metabolites. However, we still have a limited understanding of cellular targets for many of the priority chemicals on the Superfund list. Project investigators are taking advantage of the conservation of basic metabolic pathways and fundamental cellular processes between the yeast S. cerevisiae and humans to identify candidate human susceptibility genes. They are using a new approach to discover these targets in yeast and human cells using parallel deletion analysis (PDA) and RNA interference (RNAi), respectively. Deletion strains for almost every yeast gene enable new approaches to determine in parallel (PDA) the relative importance of each yeast gene for susceptibility (sensitivity) to a chemical toxicant. They are endeavoring to identify candidate susceptibility genes for selected priority Superfund chemicals that require metabolic activation including benzene, polycyclic aromatic hydrocarbons (PAHs), halogenated aliphatic hydrocarbons, and for selected metals such as arsenic and cadmium, which do not. Project investigators select and prioritize likely human candidate genes by computational analysis of the yeast data sets. The candidate human susceptibility genes are silenced in appropriate human cell lines using RNAi so that their roles in sensitivity to cytotoxicity, genotoxicity and epigenetic effects of the Superfund chemical and/or its metabolites can be evaluated. The investigators believe that this approach will identify genes that confer human susceptibility to Superfund chemicals and their metabolites and will enable future work to examine associations between variants in these genes and adverse outcomes. In addition, this work will likely provide important insights in the cellular processes leading to toxicity for priority Superfund chemicals.

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