Duke University’s RNAi Facility, which was established in 2005 to expand university researchers’ access to the gene-silencing technology, has purchased a custom-made Velocity 11 system that will allow the facility to perform genome-wide screening experiments, RNAi News has learned.
Earlier this month, the core facility received a $276,599 grant from the National Center for Research Resources to purchase the instrument system, which will provide “the automation required for RNAi library formatting, plate handling, liquid dispensing, plate sealing, and plate identification/management,” according to the grant’s abstract.
The system was pre-configured by Velocity 11, which was acquired by Agilent Technologies in December, “for the multiple workflow options necessary to maintain and deliver siRNA libraries via lipid-based transfection or viral-based transduction of mammalian cells, while maintaining the flexibility to be useful in small-molecule library screening,” the abstract adds. Once installed, it will “complete the suite of tools necessary to make whole-genome, RNAi-based screening a reality for the Duke research community.”
The grant will also be used to purchase a Baker BioProtect bio-containment enclosure for use with the instrument system.
James Pearson, manager of the RNAi Facility, told RNAi News this week that the system is expected to be in place by June, at which point the facility will run a series of pilot screens in order to “fully vet our standard operating procedure so that when we do start providing [screening services], we can ensure the product will be there.
Noting that “we don’t want to have any guinea pigs other than ourselves,” he said that the first pilot study is likely to involve the research of Duke Professor Mariano Garcia-Blanco, who is also the director of the RNAi Facility and the Duke Center for RNA Biology.
One of Garcia-Blanco’s interests is the alternative splicing of the fibroblast growth factor receptor-2 transcripts and how it is involved in prostate cancer progression, Pearson explained.
“We have fluorescent reporter constructs that report alternative processing [and] we will be screening for genes involved in the alternative splicing of FGFR2,” he said. “That will likely be the first screen that goes through.”
Although Pearson said he expects the RNAi Facility will be conducting screening experiments for other Duke investigators before the end of the year, he cautioned that it will likely take some time for these projects to get underway.
“The most important and often misunderstood aspect of any screen is the assay system,” he explained. “It will take most [researchers] several months to get their assay system robust enough that we would feel it’s worthwhile to pursue a whole-genome screen.”
He said that the facility will work with investigators to develop their assays and is currently “in the process of looking over different assays that people have come to us with … to evaluate whether they’re going to be amenable” to the Velocity 11 system.
‘Not Terribly Mature’
The RNAi Facility was set up about three years ago by Duke’s Institute for Genome Sciences and Policy, as well as the Duke Center for RNA Biology and the Duke Comprehensive Cancer Center, after the university recognized the “need for some expertise in RNA interference [to help researchers] to do larger-scale projects, things that are beyond the scope of an individual investigator,” Thomas Burke, director of IGSP technologies, told RNAi News.
Initially, it acted as a sort of clearinghouse for Open Biosystems’ Expression Arrest whole human genome shRNA library, which was developed by Cold Spring Harbor Laboratory’s Greg Hannon and Harvard University’s Stephen Elledge and includes roughly 62,500 shRNA constructs targeting more than 25,000 human genes.
The overall goal is to provide “single-well, high-content, whole-genome siRNA screening. That’s really where the power is and that’s where the field is moving.”
However, the establishment of the core facility also set the framework for the overall goal of providing “single-well, high-content, whole-genome siRNA screening,” Pearson said. “That’s really where the power is and that’s where the field is moving.”
“RNAi is a technology that is being used very broadly … [but] to use it as a screening tool is something that is not terribly mature,” Burke added. As such, the RNAi Facility began ramping up its infrastructure to be able to conduct large-scale loss-of-function studies.
By the end of 2007, the facility had purchased a Cellomics ArrayScan Vti high-content cell-based imaging suite for image acquisition and analysis, and had obtained access to Qiagen’s siRNA library covering the entire human genome.
Now, with the NCRR funding, the facility is preparing to add the Velocity 11 system, which is “the last piece of infrastructure we need in order to implement the Qiagen library,” Pearson explained.
“What [the system] does is allow us to re-format the stock plates and assay plates in a sterile environment, [as well as] seal, barcode, manage, and track them” in addition to providing a “mechanism for transfection,” he said.
While the RNAi Facility already offers assistance to Duke investigators on their RNAi experiments, Burke said that he expects a much greater level of interaction once the Velocity 11 system is installed and the large-scale, whole-genome screens are being run.
“It won’t work like a sequencing core facility where you drop off your DNA and get data back in a couple of days,” he said. “It’s something that is going to [involve] close collaboration with the investigators,” especially when it comes to optimizing their assays.
“That’s the first and hardest part of a whole-genome screen,” Pearson noted. “The screening really isn’t that difficult. It’s the assay system that has to be robust.”
Duke isn’t the only research institute aiming to improve its investigators’ access to cutting-edge RNAi technologies.
As reported by RNAi News, the National Institutes of Health recently launched an RNAi initiative that aims to help intramural investigators conduct moderate-throughput and high-throughput RNAi screens. In December, the NIH held a one-day meeting to solicit information from representatives from RNAi reagent and tool companies on how best to achieve this goal (see RNAi News, 12/20/2007).
In an e-mail sent out to the meeting’s participants, a representative from a consulting group working for the NIH said that that agency is seeking pricing information from potential RNAi reagent vendors.
Brian Oliver, chief of the developmental genomics section of the National Institute of Diabetes and Digestive and Kidney Diseases and member of a committee established to oversee the RNAi initiative, told RNAi News this week that the NIH’s scientific advisors are currently examining their options based on feedback from vendors, as well as the discussions and presentations from the meeting.