Applications of DNA Microarrays in Toxicology

Abstract

DNA microarray is a powerful tool that uses genome sequence information to analyze the structure and function of tens of thousands of genes at a time. A microarray is typically defined as a collection of microscopic spots arranged in an array or grid-like format and attached to a solid surface or membrane. These spots typically referred to as probes, are designed such that each probe binds a specific nucleic acid sequence corresponding to a particular gene through a process termed hybridization. The sequence bound to a probe, often referred to as the target, is labelled with some kind of detectable molecule such as a fluorophore. The level of binding between a probe and its target is quantified by measuring the fluorescence or signal emitted by the labelling dye when scanned. This signal provides a measure of the expression of the specific gene containing the target sequence. There are two main DNA microarray technological platforms, spotted arrays and in-situ oligonucleotide arrays, each has unique characteristics.

Each Microarray experiment typically follows several steps in defined order, array fabrication, target preparation, hybridization, signal detection and visualization, and data processing and analysis. DNA microarray-based techniques have been applied in identification of biomarkers, screening of single nucleotide polymorphisms, detection of pathogens and factors related to their virulence and drug resistance, detection of chromosomal abnormalities, detection of monogenic disease-related mutation, identifying genes linked to multi-step development process of cancer and genes related to drug abuse, in forensic chemistry and in food sciences. In many cases, they allowed accurate and rapid results. Also, Microarrays are becoming routine procedures in pharmaceutical companies replacing many conventional techniques. Microarrays have been found to provide useful information in the different stages of the drug discovery process. The potential of DNA microarray technology to identify gene expression changes associated with toxic or pharmacologic processes has been the focus of several studies. Acetaminophen, arsenic, clofibrate, methapyrilene and carbon tetrachloride are known to be hepatotoxic. DNA microarrays had been used to identify gene expression profiles of those hepatotoxicants leading to a better understanding of the molecular basis of their hapatotoxicity. Also, Microarrays were used for identification of candidate molecular markers of kidney toxicity. Also, the mechanisms of ochratoxin that is known to cause severe nephrotoxicity in animals and humans, marked changes were detected for genes involved in DNA damage response and apoptosis, response to oxidative stress, and inflammatory reactions. Neurotoxins such as lead, dopamine, dieldrin, methylazoxymethanol and nitrogen mustard are widely used substances. However, the molecular mechanisms underlying their neurotoxicity are not fully characterized. DNA microarrays had been used to identify altered gene expression following these neurotoxins to identify potential mechanisms of their neurotoxicity.