Superfund Research Program
Project Leader: Angeline S. Andrew
Grant Number: P42ES007373
Funding Period: 2005-2008
The goal of Core D is to assist SBRP investigators in the most efficient and productive manner in the areas of toxicogenomics and bioinformatics. The Core assisted Projects Arsenic as an Endocrine Disruptor, Arsenic Epidemiology, Biomarkers and Exposure Assessment, Trophic Transfer of Toxic Metals in Aquatic Food Webs, and Arsenic and ABC Transporters with toxicogenomic assay design, microarray experiments (Aim 1), and microarray data analysis (Aim 2). They have confirmed a subset of these changes at the gene and protein levels (Aim 3). The research team continues to aid interpretation of high throughput data in the context of biological pathways by generating pathway diagrams demonstrating gene regulation in the context of other cellular components. Mice exposed to arsenic in drinking water (0, 0.1, 1, 50 ppb) had statistically significant expression changes for transcripts involved in angiogenesis, lipid metabolism, oxygen transport, apoptosis, cell cycle, and immune response (Andrew, Tox. Sci, 2007). Human lymphocytes from the high vs. low exposure population groups in New Hampshire had statistically significant expression differences that were involved in defense response, immune function, cell growth, apoptosis, regulation of cell cycle, T-cell receptor signaling pathway, and diabetes (submitted).
The Core has also optimized protocols and developed tools to conduct a comprehensive analysis of somatic alterations in a set of human tumors by overlaying epidemiologic data (gender, smoking status, occupation, toenail metal levels, exposures) with full-spectrum alteration analyses in formalin fixed paraffin embedded (FFPE) tissue samples: DNA - chromosome insertion/deletions, mutation data; RNA – gene expression levels; - protein – immunohistochemical staining (Aim 4). This will allow them to utilize epidemiologic study subject tissues with extensive exposure characterization in molecular diagnostic and prognostic marker studies. They optimized labeling protocols for running Agilent Comparative Genomic Hybridization (CGH) arrays on FFPE derived tissue at Dartmouth. Their validation studies show good concordance between FFPE and fresh/frozen tissue samples. The Core has become one of the first labs to use this technique to systematically identify insertions/deletions in FFPE derived human tumor DNA. They also utilized a new gene expression cancer microarray (DASL, Illumina) that is specifically designed for shorter pieces of RNA to find expression differences associated with arsenic exposure in human tumors.
Other work in collaboration with the Arsenic Epidemiology, Biomarkers and Exposure Assessment project has centered on assessing whether genetic variations modify the toxic effects of arsenic. As described in their recent publication (Andrew, Human Heredity 2007), they are using a multifaceted analytical approach that includes logistic regression, multifactor dimensionality reduction, and hierarchical interaction graphs, Classification and Regression Trees (CART) and logic regression for the analysis of gene–gene and gene–environment interactions. Dartmouth recently acquired an Illumina Beadstation, which will greatly expand our genotyping capabilities.
Thus, the Biomarkers Core currently provides a unique combination of inter-disciplinary expertise in bioinformatics, biostatistics, genomic and proteomic skills integrated by a tight collaborative network. The current goal is to use the Biomarkers Core analytic pipeline for Superfund investigators as a model for an expanded “Integrated Biology” program that coordinates the molecular biology, genomics, proteomics, bioinformatics and biostatistics services into a more seamless approach to biomedical investigations at Dartmouth.