Thermo Fisher Scientific (www.thermofisher.com) is marrying its automation platforms with its robust reagent libraries and discovery infrastructure to develop an integrated platform for genome-wide RNAi screening with siRNAs and miRNA reagents.
Traditionally, researchers would screen RNAi reagents against specific pathways of 15–20 genes whose inhibition may be important. Thermo Fisher now lets them screen against the approximately 22,000 genes in the human genome. The benefits, according to Dave Evans, Ph.D., senior director of RNAi discovery and therapeutic services, include gaining a more rapid understanding of the role specific genes play in disease mechanisms.
Application of high-content screening lets researchers look at subcellular effects induced by silencing individual genes or use end-point analysis to provide insight into the role these genes play in global parameter such as cell viability, Dr. Evans explains.
“One of the biggest problems in the industry is that drugs may not specifically target the appropriate mechanisms to induce therapeutic benefit across a large patient population, so many drugs fail in the clinic,” Dr. Evans says. Genome-wide RNAi screening, in contrast, helps researchers identify nodes in specific pathways where therapies against these targets may have a more profound effect.
“By combining the use of RNAi with coexposure to a drug, new targets can be discovered that, when silenced, synergize with and improve the potency and/or efficacy of the existing drug. Such adjunct targets have been identified for cancer therapeutics such as Doxorubicin or the taxanes. By identifying targets that synergize with an existing drug, the dose can be reduced, which also may reduce unwanted side effects.”
Understanding and characterizing the mechanisms that lead to improved therapeutic benefits aid in repurposing failing drugs. “This approach is becoming part of the standard tool set in drug discovery,” Dr. Evans says, “but we’ve just scratched the surface with the technology.”
miRNAs, either mimics or inhibitors, can be assayed with this technology too. They are becoming important in the differentiation and maturation of a wide variety of cell types, particularly stem cells, and they are generating interest in cancer and schizophrenia as well as other diseases.
Affymetrix (www.affymetrix.com) will be discussing its GeneChip® Array Station at the conference. The combination of the GeneChip Array Station and the GeneChip HT Array Plate Scanner increases workflow throughput and standardization, eliminating the variability inherent with human technicians, according to Shantanu Kaushikkar, product marketing manager for systems and software.
This combination lets researchers replace a single column approach with a 24- or 96-well plate, he says, explaining that although the technology has been used in research for a while, “the adoption rate is just starting to ramp up.”
The Affymetrix GeneChip Array Station is a dual-purpose instrument that automates target prep and array processing for high-throughput array plates, allowing a gradual scale-up without increasing staff size. It prepares a hybridization cocktail that can be added easily to the existing workflow, Kaushikkar says, letting researchers analyze 96 individual samples simultaneously.
The GeneChip HT Array Plate Scanner scans 24- and 96-well array plates for human, mouse, and rat samples. It focuses and scans each array in less than three minutes, according to Kaushikkar. It also boasts a dual-core processor in its computer workstation; an internal, automatic barcode reader; and software for data analysis and visualization.
These combined systems offer significant value in terms of standardization, Kaushikkar notes. Automation reduces variability by ensuring the same methods are applied to each set of samples regardless of where they are run or who runs them. The result is more consistent, higher-quality data that can be automatically tracked and added to the lab’s information management system.
“We have an open platform, which distinguishes us from others,” Kaushikkar adds. As an example, he notes that the target prep can be performed on hardware from Beckman Coulter (www.beckman.com), and data from the acquired images can be analyzed with software applications from a variety of vendors.