Drosophila RNAi Screening Center Flies into the Future

More than 35 research teams from as far away as Israel, France, and Argentina and as near as the HMS Quad have visited the Drosophila RNAi Screening Center since it opened in June 2003. The facility enables scientists to look for genes of interest or investigate pathways within fruit fly cells. The center’s genomewide library of Drosophila double-stranded RNAs (dsRNAs) makes the investigations possible since these sequences block production of specific proteins through RNA interference (RNAi). The screening center, first opened by Howard Hughes researcher Norbert Perrimon, HMS professor of genetics, and now led by HMS associate professor of pediatrics Bernard Mathey-Prevot, has steadily expanded its utility to the scientific community through technology improvements, RNAi library upgrades, and continued broad accessibility.

Photo by Graham Ramsay Bernard Mathey-Prevot (left) and Nadire Ramadan have shepherded more than 35 research teams through the Drosophila RNAi Screening Center, which recently acquired a high-throughput confocal microscope that will be available to researchers beginning this month.

The center in partnership with the Perrimon lab recently acquired, with funding from the Howard Hughes Medical Institute, a powerful high-throughput confocal microscope, the Evotec Opera High Content Screening System. Only a handful of these exist in the United States, and all but the center’s are industry-owned. “This one is available to the scientific community with no strings attached,” said Mathey-Prevot.

The clarity, accuracy, and power of visual information obtained with this machine make it ideal for research in systems biology, defining interconnected pathways in a cell. The previous automated microscope available at the center examined the entire depth of a cell monolayer simultaneously, while the Evotec Opera can visualize discrete cross-sections. A protein in the cell cytoplasm, for example, that is hovering above the nucleus might appear as though it were in the nucleus with the older system, but the new machine reveals its true location. The center obtained the Evotec Opera in June, began its first test screen in mid-August, and will make the machine available to researchers in September. The confocal microscope scans a 384-well plate in six minutes compared to the 20 to 30 minutes it took on the center’s older system. “This machine is moving us into a different league with regard to high-throughput screening” said Perrimon.

Additional improvements in the center’s research capabilities originated from analysis of their database, a compilation of results from 30 completed screens. Using this pooled data for quality-control purposes allowed the center to identify potential off-target effects, which can occur when a dsRNA has homology with unintended genes. The scientific community had previously recognized the problem of off-target effects in mammalian cell research, but mistakenly thought it inconsequential in Drosophila. The screening center’s switch to a second-generation RNAi library last fall was specifically intended to minimize the false positives due to off-target effects. This change emphasizes the “importance of a centralized facility in helping to recognize and fix a problem,” said Mathey-Prevot.

The center also has seen growth in the pool of scientists who find its capabilities applicable to their research. A growing trend has some mammalian cell scientists visiting the center as an efficient way to advance research in human disease. Two research groups, led by HMS professors Anjana Rao and Jean-Pierre Kinet, set out independently to find a long-sought mammalian protein by first looking at Drosophila then identifying the human homologue. Mathey-Prevot recognizes the uncharacteristic nature of human-disease researchers taking this step. “It took some guts for them to say, ‘I don’t think this will be a waste of time,’” he explained. “It was a gamble, and we’re grateful to those researchers willing to take that gamble. It is a very valuable approach that has paid off handsomely for them.”

The screening center’s growing collaboration with the ICCB-Longwood Screening Facility, which just began offering similar screens in mammalian cells, also enhances the center’s utility to mammalian cell researchers. “In the long term, we’d like to work out a relationship between the two centers and combine these two approaches; I think that will have a lot of power,” said Mathey-Prevot.

To perform a screen at the Drosophila RNAi Screening Center, researchers must submit an application and show they have optimized their assay methods prior to visiting the facility. The center’s egalitarian ethos makes it accessible to any researcher, inside or outside Harvard, from very small labs to high-profile groups. “It allows anyone with regular funding to be invited to the same table,” said Mathey-Prevot. “It’s a level playing field for everyone.” Additional information is available at http://flyrnai.org.

—Kathleen Fink

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