Technology Advances
Slicing the Genome Pie
Although tracking an entire genome for drug targets sounds alluring, it’s still just too much molecular “pie” to examine, unless researchers find ways to slice it. For example, Emily LeProust, PhD, Agilent Technologies, Santa Clara, Calif., R&D chemistry manager, genomics, says, “In target identification, SNP studies are yielding valuable information about potential genomic variation associated with diseases.” But, she adds, “Follow-up sequencing studies are necessary to characterize the extent of such mutations in the identified genomic locations—that is, beyond only the SNP—and for large sample sets.” Moreover, says LeProust, taking a whole-genome approach to such studies is not realistic.
To take on that challenge, Agilent is developing products that partition genomic regions—letting scientists basically pull out regions of interest. “The primary method, based on a technology developed by the Broad Institute, employs long, biotinylated RNA probes prepared by Agilent to first hybridize to the relevant portion of sheared DNA samples, then to physically separate them from the rest of the sample—using Steptavidin-coated magnetic beads—and finally to release them in solution,” explains LeProust. With only a few micrograms of DNA, researchers can use this technique to pull out several megabases of DNA. Moreover, scientists can then study specific slices of the genome in the hunt for better targets.
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Although microRNA (miRNA) seems involved in everything already, even more applications lie ahead. “Altered expression of particular miRNAs has been implicated in the onset and development of cancer and other disease states,” says Amy Cuneo, manager of product development for epigenetics at Invitrogen Corporation, Carlsbad, Calif. Consequently, such changes in miRNA expression could be targeted as biomarkers for diagnosing a disease. Cuneo also points out that miRNAs might participate in the suppression of tumors or as oncogenes. “This makes them very interesting targets for potential therapeutics,” she says, “because it’s possible to inhibit or mimic these key miRNAs in order to alter non-coding RNA profiles or target messenger RNAs or proteins of genes that may also be involved in the particular cancer or disease.”
Turning miRNAs into diagnostic or therapeutic targets, however, depends on identifying the crucial miRNAs. To help researchers with that step, Invitrogen just released its NCode Human miRNA Array V3. Christopher Adams, PhD, research area manager for epigenetics at Invitrogen, says, “In addition to updating the Sanger miRBase content present on the V3 array, we have added 373 putative novel miRNA probes derived from analysis of deep sequencing data.” Moreover, Invitrogen selected biologically-validated miRNAs as those “putative” probes. As a result, says Adams, “We see a dramatic increase in detection rate and biological relevance. From internal research and external collaborations, we have already seen numerous sequences from the novel content associated with tumors and other disease states.” This miRNA array also comes with NCode Profiler software, which Cuneo describes as “an advanced experimental design and analysis solution for two-dye expression profiling microarray experiments.”
Like other microarrays, NCode Human miRNA Array V3 provides only semi-quantitative results, so researchers can follow up with qRT-PCR. Cuneo says, “Our NCode SYBR Green and NCode SYBR GreenER miRNA qRT-PCR kits can actually be used to look at expression levels of these—or any—novel RNA sequences.” Although some commercial qRT-PCR products use miRNA-specific primers that require a publicly-available sequence of the miRNA, Cuneo says that the Invitrogen qRT-PCR products get around this problem through a process that ultimately uses the miRNA of interest as the target-specific PCR primer.
With this combination of technologies, miRNA could be used to more easily find new diagnostic or drug targets and quantify the results.
About the Author
May is a publishing consultant for science and technology based in Minnesota.
This article was published in Drug Discovery & Development magazine: Vol. 11, No. 7, June, 2008, pp. 12.
