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NIEHS Microarray Group Hosts Genomics Day

By Laura Hall
October 2009

Bushel, a staff scientist in the Biostatistics Branch, talked about the tools available to analyze microarray data and publishing datasets in the Gene Expression Omnibus repository of the National Center for Biotechnology Information (NCBI).
(Photo courtesy of Steve McCaw)

Brian Chorley, a postdoctoral fellow in the Environmental Genomics Group, explained the chromatin immunoprecipitation technique with the microarray format he used to find novel NRF2 binding sites. (Photo courtesy of Steve McCaw)

Lindsay Smith, a predoctoral IRTA fellow in the Molecular Endocrinology Group, used microarrays to find the first evidence of altered microRNA expression during glucocorticoid-induced apoptosis.
(Photo courtesy of Steve McCaw)

Gerrish, foreground, introduced Stephanie Lahousse, Ph.D., a postdoctoral fellow in the Molecular Pathology Group, who used microarrays in her two year carcinogenecity study of hepatocellular adenoma and carcinoma in oxazepam-exposed mice.
(Photo courtesy of Steve McCaw)

NMC Core Director, Rick Paules, Ph.D., left, listened as Scott Auerbach, Ph.D., a postdoctoral fellow in the Toxicology Branch, explained how microarrays were used to develop a gene expression-based predictive model to identify hepatocarcinogens -- a potential way to prioritize chemicals for carcinogenecity studies.
(Photo courtesy of Steve McCaw)

NIEHS Genomics Day, held on September 1, offered scientists at NIEHS and visitors an afternoon of talks by investigators and trainees, a poster session, and an opportunity to learn more about the NIEHS Microarray Laboratory. Attendees also had a chance to talk to vendors about new microarray products and instrumentation. In his opening remarks, moderator Kevin Gerrish, Ph.D., technical laboratory manager, said the Microarray Group organized this event to ensure that intramural researchers were aware that "we do more than gene expression."

There have been many changes since the last Genomics Day in 2004. Rapid technological advances in microarray capabilities and the acquisition of three commercial platforms have greatly expanded the types of research that can be done through the facility. Gone are the days when the group made its own microarray slides. "We found that it was much more efficient to just buy the commercially available arrays," observed Gerrish.

Scientists no longer need to worry about limited choices in microarrays. Agilent, Affymetrix and now Illumina, the three platforms available, are able to provide microarrays that cover analyses from "plant species to Caenorhabditis elegans to bacteria to even zebrafish - almost every model organism that I've run across here," said Gerrish. He explained that in the rare situation that an investigator needs a custom arrray, most of the suppliers will work with the scientist to create one.

According to Gerrish, the types of studies that can be done with microarrays have expanded as well. The traditional gene expression studies allow screening across an entire genome for disease biomarkers or effects of environmental agents. Now, researchers who use the Microarray facility can explore the mechanisms that regulate gene expression utilizing array-based techniques.

Investigators can assay protein-DNA interactions with chromatin immunoprecipitation (ChIP-chip), genetic variation with array-based comparative genomic hybridization, a method that surveys DNA copy-number across an entire genome, and single nucleotide polymorphisms (SNPs). SNPs can affect disease susceptibility and effectiveness of drug therapies. SNPs can also be used to study loss of heterozygosity (LOH), an allelic imbalance in which there is a complete loss of one allele or an increase in copy number of one allele relative to the other. LOH occurs in many human cancers.

Arrays can be used in studies of epigenetics, looking at heritable changes not in the DNA sequence, and microRNAs (miRNAs) -- short non-coding RNAs that regulate gene expression.

Research using microarrays generates vast quantities of data requiring bioinformatic software for analysis. Biostatistician Pierre Bushel, Ph.D., talked about the Microarray and Genome Informatics (MGI) service provided to NIEHS scientists to help with analyzing microarray data. The MGI uses commercial and in-house custom software and can assist the researcher in data processing and database management.

To give the audience a sampling of the types of research projects utilizing microarrays, Gerrish invited four trainees to discuss their research (see text box). The poster session following the talks gave NIEHS scientists an opportunity to have in-depth discussions about microarray techniques and applications. Other members of the Microarray Group - Rick Fannin, Danica Andrews, Stella Sieber and Laura Wharey - were on hand during the poster session to answer questions.

(Laura Hall is a biologist in the NIEHS Laboratory of Pharmacology currently on detail as a writer for the Environmental Factor.)

Reuben Thomas, Ph.D., left, a postdoctoral fellow in the Environmental Systems Biology Group discussed his poster with Min Ok Song, Ph.D., center, and Chang-Ho Lee, Ph.D. Numerous investigators in the NTP and the NIEHS Division of Intramural Research, as well as a few vendors, presented posters at the event.
(Photo courtesy of Steve McCaw)

Trainees' Presentations Showcase the Value of Microarrays in Research

  • Brian Chorley, Ph.D., used ChIP-chip to identify novel genomic binding locations for a transcription factor of interest, nuclear factor erythroid-derived 2-like 2 (NRF2). NRF2 senses and responds to oxidative stress by binding to antioxidant response elements (AREs), many of which are unknown. Chorley found many genes displayed both NRF2 binding in their promoter and gene induction by NRF2 -- over half of these genes had not previously been described as being regulated by NRF2.
  • Lindsay Smith''s studies on glucocorticoid-induced apoptosis led her to use microarrays to discover that miRNAs were differentially regulated by glucocorticoids in rat thymocytes. Cells treated with dexamethasone, a glucocortocoid receptor agonist, had widespread downregulation of miRNAs.
  • Matthew McElwee, a graduate student in the Comparative Genomics Group, examined the molecular mechanisms of mercury toxicity comparing the effects of inorganic mercuric chloride (HgCl2) to organic mercury, methyl mercury chloride (MeHg), in the gene expression pattern of Caenorhabditis elegans using microarrays. He found some similarities, but more often very different transcriptional responses between the two forms of mercury.
  • Stephanie Lahousse compared the gene expression of normal mouse liver and oxazepam-induced liver tumors using microarrays. Lahousse found differences in over 1500 genes, including genes involved in oxidative stress, the wnt signaling pathway, DNA methylation, and histone modification.

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