The utility of DNA microarrays for characterizing genotoxicity - Genomics and Risk Assessment: Mini-Monograph

Environmental Health Perspectives, March 15, 2004 by Ronald K. Newton, Marilyn Aardema, Jiri Aubrecht

Microarrays provide an unprecedented opportunity for comprehensive concurrent analysis of thousands of genes. The global analysis of the response of genes to a toxic insult (toxicogenomics), as opposed to the historical method of examining a few select genes, provides a more complete picture of toxicologically significant events. Here we examine the utility of microarrays for providing mechanistic insights into the response of cells to DNA damage. Our data indicate that the value of the technology is in its potential to provide mechanistic insight into the mode of action of a genotoxic compound. Array-based expression profiling may be useful for differentiating compounds that interact directly with DNA from those compounds that are genotoxic via a secondary mechanism. As such, genomic microarrays may serve as a valuable alternative methodology that helps discriminate between these two classes of compounds. Key word:." biomarkers, gene expression profile, genetic toxicology, mechanism of action, toxicogenomics. Environ Health Perspect 112:420-422 (2004). doi:10.1289/txg.6709 available via bttp://dx.doi.org/[Online 15 January 2004]

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Genetic damage elicits stress-related responses that may alter the expression of genes associated with numerous biological pathways (Hollander and Fornace 1995). It has been proposed that patterns of induced gene expression changes may be characteristic of specific classes of toxic compounds and that distinctive fingerprints may be identified that help classify agents with different mechanisms of action (Hamadeh et al. 2002a, 2002b; Waring et al. 2001a, 2001 b). Historically, the expression of bacterial SOS response genes was used for detecting genotoxicity of chemicals. The bacterial DNA repair pathways have been well characterized, and various genes have been used as indicators of the SOS response. In these assays (Ben-Israel et al. 1998; Nunoshiba and Nishioka 1991; Oda et al. 1985; Ptitsyn et al. 1997; Quillardet et al. 1982), the transcriptional activities of SOS response-associated genes have been detected using promoter-reporter constructs (biosensors). Thus, each bacterial tester strain carried a construct capable of detecting induction of a single SOS-response pathway. An array of cell lines covering multiple genotoxic stress-associated pathways provided even more insight into bacterial genotoxic mechanisms. A similar approach also has been applied to human cells using an array of HepG2 cell lines carrying genotoxic stress-associated promoter or response element-reporter gene fusion constructs (Todd et al. 1995). The simultaneous treatment of these cell lines provided a genotoxic stress-associated gene expression profile in human cells exposed to various chemicals (Todd et al. 1995) and environmental pollutants (Vincent et al. 1997). In drug discovery, the array of cell lines has been used successfully in the study of the mechanism of genotoxicity of organometallic cytostatics (Aubrecht et al. 1999). However, recent development of oligonucleotide and cDNA microarrays for large-scale parallel gene expression profiling will make the cell-based promoter-reporter arrays obsolete. In contrast to biosensor cell lines that cover a limited number of biological pathways, gene expression microarrays allow measurement and characterization of genomewide gene expression changes in a single experiment. As such, toxicogenomic studies are expected to have a large impact on the field of genetic toxicologys as discussed by Aardema and MacGregor (2002).

In this overview we provide a summary of research activities of the Genotoxicity Working Group of the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) Committee on the Application of Genomics to Mechanism-Based Risk Assessment. A description of the overall objectives and design of the committee is included in this mini-monograph (Pennie et al. 2004). The HESI Genotoxicity Working Group is an international collaborative effort that includes scientists from industry, academia, government, and regulatory agencies (Table 1). The major objective of the collaborative project was to evaluate the utility of gene expression profile analysis for risk assessment of genotoxicants. The group analyzed gene expression profiles of compounds with known mechanisms of genotoxicity to determine whether compounds from different mechanistic classes display distinct gene expression profiles. Particular focus was on identifying genes that discriminate between non-DNA-interactive compounds (initial target is not DNA) from DNA-interactive genotoxicants. By examining compounds with known mechanisms and well-characterized mutagenic activities, we attempted to address the issue of whether gene expression changes provide useful information for understanding how a compound exerts its genotoxic effects. Other important components of our evaluation were to ensure that one could distinguish a genotoxicity profile from a cytotoxicity profile and to evaluate the value of the technology for examining low-dose effects of genotoxic agents. The Genotoxicity Working Group also examined the correlation of measured gene expression changes via microarrays with traditional genetic toxicology end points. Similarly, a secondary question was whether microarray technologies could be a useful adjunct to the standard genotoxicity test battery.