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Final Progress Reports: University of California-Berkeley: Genomics and Analytical Chemistry

Superfund Research Program

Genomics and Analytical Chemistry

Project Leader: Daniel K. Nomura
Co-Investigator: Martyn T. Smith
Grant Number: P42ES004705
Funding Period: 2006-2017
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Final Progress Reports

Year:   2016  2010 

The Toxicogenomics Laboratory Core provides a centralized source of specialized facilities and equipment, services, well-tested collection and storage protocols, and expert technical support using the latest "-omics" technologies and analytical instruments for project investigators. These services greatly enhance the ability of project investigators to achieve their overall goals.

Overall goal

The goal of this laboratory core is to provide the infrastructure and expertise for several projects to achieve their goals. The overall goal of the program is to apply functional genomics, proteomics, transcriptomics, and nanotechnology to better detect arsenic, mercury, benzene, polycyclic aromatic hydrocarbons, trichloroethylene, and other Superfund priority chemicals in the environment; evaluate their effects on human health, especially the health of susceptible populations, such as children; and remediate their presence and reduce their toxicity. Projects 1 - 4 (Biomarkers of Chemical Exposure and Leukemia Risk; Functional Profiling of Susceptibility Genes; Arsenic Biomarker Epidemiology; and Application of Comparative Genomics, Transcriptomics, and Proteomics to Optimize Microbial Reductive Dehalogenation) use functional genomics, proteomics, and transcriptomics in their studies. Further, Projects 1 and 3 are epidemiological studies that require sophisticated sample processing so that these technologies can be applied. The success of Projects 1 - 4 largely depends on the effective handling and management of biological samples, as well as access to--and expertise in--the latest "-omic" technologies. Thus, detailed collection and storage protocols have been designed and Core facilities provided for the cytogenetic, genotyping, gene expression and proteomic analyses proposed in Projects 1 - 4.

Important accomplishments so far

The Core has processed, maintained, and stored biological samples and cell lines; provided facilities and methodologies for cytogenetic analysis (study of chromosome structure); provided facilities for gene expression profiling using Affymetrix, Illumina, and custom array technologies; provided facilities for proteomic analyses using various mass spectrometric technologies; and provided facilities and methodologies for the analysis of genetic polymorphisms by Taqman-based and bead array technologies using the ABI 7900 Sequence Detection System and Illumina Bead Station platforms.

Accomplishments for the last year

The Core conducted protein expression profiling in arsenic target cell lines to help identify candidate biomarkers of response to arsenic, thereby helping to elucidate the mechanisms of arsenic toxicity. The most significantly altered peptides were chosen for protein identification via mass spectrometry. To follow up, they performed analyses to confirm the identified expression changes of 3 proteins, HSPA5, MCM6, and GNB1, which are involved in protein folding, DNA replication, and signal transduction, respectively. For this, they treated human HK-2 kidney cells and HOK-16B keratinocytes to both inorganic arsenic and MMA, a toxic, methylated form of arsenic found as a common metabolite in the human body.

What they plan to do next

Future experiments will involve 2D DIGE analysis on cells exposed for multiple time points and multiple biologically relevant concentrations of arsenic to determine the specificity of response to treatment, followed by measurement of expression changes in urine specimens from children exposed to high and low levels of arsenic.

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