Project 2: Comparative and Functional Genomics Analysis of Superfund Toxicants

University Of California, San Diego, La Jolla CA

Investigators

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Abstract

Project 2 will use functional toxicogenomics and proteomics technologies to uncover the genes and pathways that determine cellular responses and genetic susceptibilities to arsenic, cadmium, chromium, nickel and other heavy metals that contaminate Superfund sites. Comparative functional genomics will provide key insights into some of the basic mechanisms that determine resistance or sensitivity to heavy metal toxicants. These studies are divided into three Specific Aims: 1) Assemble a functional genomic profile of fission yeast using a panel of environmental toxicants assessed with haploid and diploid deletion libraries. Barcode analysis determined by deep sequencing will provide a detailed and quantitative picture of the genes that determine susceptibilities to heavy metals. Cluster analysis will be applied to toxicants tested in pure forms or in mixtures. 2) Build on the functional genomic profiling data by assembling epistatic miniarray profiles (E-MAPs). These mutant interaction studies will define the genetic networks that determine cellular sensitivities to heavy metals and may uncover interactions with other pathways such as DNA damage responses (DDRs). The existence of conserved genetic interactions in human cells will be assessed by RNAi analyses. 3) Investigate changes in protein abundance triggered by heavy metal exposure using isobaric tag for relative and absolute quantitation (iTRAQ). These proteomic studies will provide further insights into how stress-regulated transcription factors and stress-activated protein kinases control cellular responses to heavy metal stress.