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Aug 1, 2009 (Vol. 29, No. 14)

Microarrays for Gene-Expression Studies

Cost-Effective Alternative to Sequencing Boasts a Multitude of Applications

  • Characterizing Threats

    Another application of microarrays that will be explored is the characterization of emerging, unknown, and engineered threats. Crystal Jaing, Ph.D., group leader at the Lawrence Livermore National Laboratory biosciences and biotechnology division will discuss some of the work that her group is doing with microarrays in the area of biodefense. “Our team is strong on bioinformatics, and microarrays play a big part in our research,” she notes.

    PCR is limited in the number of pathogens it can analyze. “You can multiplex PCR to detect a number of pathogens, but it does not provide the throughput to analyze all possible pathogens present from one assay,” Dr. Jaing says.

    She reports that there are several applications of microarrays at work. The first involves using microarray probes developed to find viruses and bacterial agents. “The key capability is the comprehensive viral and bacterial sequences we have covered in our microarray to enable rapid metagenomic analysis of environmental and clinical samples.

    “The second microarray targets microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug-resistance profiles of unknown organisms in environmental samples. This array can provide value to the Biowatch surveillance programs by providing rapid additional characterization of positive samples.”

    There are many advantages to using microarrays in her field, but Dr. Jaing acknowledges some challenges as well. “Working with microarrays from the bioinformatics standpoint presents a continual challenge in that there are always new viruses and bacteria to keep up with, thereby, constantly needing to update the database. Though microarray prices are coming down, not every lab has the capability. It’s not like PCR, where you find it in every lab.”

    “Sequencing still provides the highest resolution, but it’s also expensive. Microarrays provide a cost-effective way to screen samples quickly, although I have to say that all three technologies work well together.”

  • Ecological Applications

    Click Image To Enlarge +
    Researchers at Indiana University are using gene-expression approaches to evaluate the use of Daphnia to study the effects of chemical threats on the environment.
    (Paul Hebert, Biodiversity Institute of Ontario)

    “There is always a lot of discussion about high-throughput sequencing versus microarrays for gene expression,” says John Colbourne, Ph.D., genomics director at Indiana University Center for Genomics and Bioinformatics. For instance, Dr. Colbourne reports that the data from Roche NimbleGen tiling-path arrays is comparable to RNA sequencing with the Illumina Genome Analyzer.

    Yet, for targeted studies that screen transcriptional changes across large numbers of conditions and for large numbers of samples, practicality becomes a central issue. “A main advantage that we see in using microarrays is that multiplexing 12 to 24 samples on a single chip can save time and money as we move toward understanding transcriptional variation at the level of populations.”

    Studies in Dr. Colbourne’s lab encompass the fields of evolutionary ecology, molecular toxicology, systematics, and functional genomics. His lab is now concentrating more on environmental issues and applying approaches traditionally used for gene expression in cancer research to environmental studies.

    “Using microarrays, we hope to be running hundreds upon hundreds of experiments in a week,” reports Dr. Colbourne.  “The limitation is that there are not enough spaces for independent trials on a single chip. NimbleGen has 12 plexes and is looking to go to 24 plexes and beyond, not just to increase single throughput but to also decrease expenses and to minimize experimental variation. Microarrays can interrogate gene profiles such that multiple samples can be processed discretely.”

    Dr. Colbourne and his team seek to connect gene expression and genome structure with individual fitness and population-level responses to environmental chemicals and natural stressors. His work revolves primarily around Daphnia as a model organism to discover the effects of chemical threats to the environment.

    “There are currently 80,000 chemicals in the environment, with an additional 2,000 introduced every year,” Dr. Colbourne says. “Less than seven percent of these get tested. We chose Daphnia because it is already a model system for monitoring the health of freshwater ecosystems. It’s a big push to discover how these genomic systems in the environment are affected by the chemicals—often, we don’t know if a chemical is safe or not. There is no systematic and inexpensive way to test the safety of chemicals in environmentally relevant conditions. Chemicals are mostly found in combinations, which is problematic, as they will interact in unexpected ways to affect the health of any animal.”

    Dr. Colbourne says that Daphnia is one of the best-characterized genomic systems. “But in 25–30 percent of any genome, you have known genes with unknown functions. Chances are these genes have condition-specific regulation in natural settings, and therefore, no effects are ever detected in the laboratory. When we succeed in routinely studying gene expression within natural populations and ecosystems, we will likely discover a much greater diversity of gene functions, and perhaps even large transcribed areas of genomes that are currently unannotated.”

    Dr. Colbourne believes that there are practical reasons to use microarrays in this way. “Regulatory agencies are anxious for new technologies that are more sensitive, less expensive, and better able to assess the potential risk of environmental chemicals to humans and to the environment. With sufficient funding to produce the required reference gene-expression databases, we should soon begin monitoring the health of Daphnia populations using microarrays, which will simultaneously diagnose the presence of chemicals in regional waters and their health effects. There are two uses of microarrays: as a chemical detection tool on sentinel species within ecosystems, and as a method to classify environmental risk based on knowing toxicological effects.”

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