Microarrays as toxin sensors.

Abstract

Microarrays can be used to identify toxin effects on gene expression, delineate detoxification pathways in vivo, and potentially as sensors to monitor human exposure. ‘Why is a raven like a writing desk?’ asked the memorable Mad Hatter in Lewis Carroll’s Alice in Wonderland, a riddle that has puzzled and amused readers for more than a century. This was not the only example of the Mad Hatter’s strange behavior at Alice’s infamous tea party. The Mad Hatter criticized Alice’s long hair, an unusually forward and perplexing criticism of a Victorian girl, and sported a wristwatch that reported the day of the month but not the time of the day. So bizarre was the episode that an exasperated Alice regarded it as the ‘stupidest tea party I ever was at’, perhaps not surprising in view of the well-documented cases of mercury poisoning that afflicted felt hatmakers in the 19 century, producing a myriad of symptoms including severe neurological dysfunction. Although Carroll’s Mad Hatter was a fictional character, the ‘mad hatter’s’ syndrome was anything but thatFso prevalent in fact that it resulted in a complete banning of mercury nitrate from the hat-making industry. Exposure to environmental toxins continues to be a challenge in industrialized countries, with more than 70 000 chemical compounds registered for use in the United States alone, and relatively little detailed information available concerning the toxicity of these compounds in humans. Organic solvents, pesticides, herbicides, and heavy metals are known or suspected contributors to cancer, birth defects, immunological disorders, and a host of neurological diseases when exposed to humans at elevated levels. Carbon tetrachloride (CCl4) is a clear, colorless, toxic liquid that enters the atmosphere in a highly efficient manner because of its high vapor pressure. The atmospheric lifetime of this stable compound is approximately 50 years. CCl4 is used commercially in dry cleaning, degreasing, and in the production of refrigerants and other chlorinated hydro-carbons, and acute human exposure via inhalation produces serious symptoms including nausea, vomiting, dizziness and headache. The liver, kidney and brain are three of the main target organs for this toxic substance, and chronic exposure in laboratory rats and mice produces embryonic lethality, hepatomas, and hepatocellular carcinoma. The stability and toxicity of CCl4 suggest the need for new tools to study and monitor human exposure to CCl4 and other environmental toxins. It is in this context that our discussion turns to a recent paper by Young et al ‘Analysis of gene expression in carbon tetrachloride-treated rat livers using a novel bioarray technology’ published in The Pharmacogenomics Journal. In a paper destined to be a classic, Young et al combine highquality microarrays, powerful computational tools, and a well-established rat model of liver toxicity to identify genes that are induced and repressed by CCl4. The expression signature identified in this study provides fresh biochemical clues to the mechanism of CCl4 toxicity in rat, and such data are likely to be informative in humans. The work also suggests a general approach for studying environmental toxins, providing a straight path to developing analytical microarrays to assess patient exposure. The paper builds on the earliest microarray publications, which demonstrated the usefulness of chips for expression profiling and toxininduced gene discovery, and in these respects the Young et al paper does not break new ground. However, in terms of all the technical details of the approach and in identifying a specific subset of CCl4-induced genes, Young’s publication is new and impressive. The paper begins with a description of microarray platforms, describing some of the pros and cons to the two main types of nucleic acid microarrays (cDNA and oligonucleotide). Young et al correctly point out that for organisms in which there is abundant sequence information, oligonucleotide microarrays offer some advantages over cDNA microarrays, including the fact that single-stranded array elements do not self-hybridize and therefore can produce stronger signals than double-stranded cDNA elements. Oligos can be designed with pinpoint accuracy against unique gene regions, essentially eliminating crosshybridization between homologous genes and providing greater assay accuracy. There are also some important differences between oligonucleotide arrays synthesized in situ and microarrays made by deposition using pins or ink jets. A major distinction between traditional arrays and microarrays is the use of fluorescence detection instead of radioisotopes, which allows a high degree of assay miniaturization in the latter case. A major difference between in situ synthesis and deposition is the ability in the latter to assess oligonucleotide quality and purity prior to microarray manufacture. The microarrays used in this study contained 1137 unique targets representing 1040 rat genes and 97 controls deposited by ink jetting. Although the The Pharmacogenomics Journal (2003) 3, 125–127 & 2003 Nature Publishing Group All rights reserved 1470-269X/03 $25.00