MP7 Toxicogenomics in Environmental Studies
Monday, 14 November 2005: 8:00 AM - 5:30 PM in Exhibit Hall

(SON-1117-567744) Changes in Transcriptome of HepG2 Cells Exposed to Copper: Pathway Mapping and Interactome Identification.

Song, M-O¹, Freedman, J. H.¹, ¹ Duke University, Durham, NC, USA

ABSTRACT- Copper is an essential trace element that serves as an important catalytic cofactor for cuproenzymes, carrying out fundamental biological functions in growth and development. It has been shown that copper has the potential to generate free radicals and oxidize cellular components through its redox activity. We have previously shown that copper activates transcription through both metal- and oxidative stress-responsive signal transduction pathways. Our hypothesis is that copper modulates the activity of multiple intracellular signal transduction pathways to affect transcription, which ultimately disrupt normal development. The differentially expressed genes after 8-h exposure to copper were grouped by the functional categories of Gene Ontology using Gene Ontology Tree Machine. Significantly enriched GO categories (p < 0.01) in biological process were: response to metal ion, copper ion homeostasis, asparagine biosynthesis and heme oxidation, and those in molecular function were cadmium binding, copper ion binding, transforming growth factor beta receptor binding, asparagine synthase activity and heme oxygenase activity. We also perform mapping of the differentially expressed genes onto biological pathways using GenMAPP, PharmGKB, KEGG and BioCarta using ArrayXPath. Eighty five of the 374 genes (600 M copper) were identified in 17 of the 45 GenMAPP, 5 of the 9 PharmGKB, 26 of the 70 KEGG, and 169 of the 346 BioCarta pathways. Pathways identified included TGF beta signaling pathway, apoptosis, MAPK cascade, glutathione metabolism, p53 signaling pathway, Ras signaling pathway and oxidative stress induced gene expression via nrf2. All these results strongly support our hypothesis. We also identified interactomes with Cytoscape. Interactomes with high module scores have genes such as PKB, SP-1, BAD, STP15 and CD28 as cores. We will perform identification of significant interactomes from transcriptomes with different exposure time and investigation of potential signal transduction pathways based on the identified interactomes.

Key words: transcriptome of HepG2, copper, pathway mapping, interactome identification