This article has been updated to include information about Life Technologies' spokesperson.
The National Institutes of Health announced this week that Life Technologies will allow the public release of all sequence data for those of its siRNAs used in RNAi screens conducted at the agency's National Center for Advancing Translational Sciences.
The unusual move by Life Tech comes amid increasing awareness of the impact that off-target effects can have on the results of RNAi screens, according to Scott Martin, group leader of RNAi screening at NCATS, which uses the company's Silencer Select human and mouse siRNAs.
"There are a number of publications out there that show, when you look at RNAi screening data and you have all the sequence information, you can clearly see that most of the phenotype that you observe in a screen is really due to off-target effects," he told Gene Silencing News.
For instance, Eugene Buehler, NCATS informatics leader and former Merck scientist, has published data showing that siRNAs that target different genes but have the same seed sequence "correlate much better in terms of activity in a screen than do different siRNAs designed to target the same gene," Martin noted. Buehler and his colleagues also reported a technique for using seed sequence commonality to identify off-target effects in siRNA screens.
By being able to include complete siRNA sequence data along with the results of an RNAi screen, others in the scientific community would not only be free to reproduce the findings, but also get a better handle on the off-target effects that may be skewing outcomes.
Individual siRNAs, when introduced into a cell, can "downregulate many dozens of genes that it is not intended to downregulate," Martin said. "The sequence information allows you to not only look at that, but helps you to determine what seeds in a particular assay give a biased effect.
"You could use that information to flag siRNAs that seem to be giving activity through these seed-based off-target effects," and apply informatics approaches to potentially interpret the unintended silencing, he said.
"Our hope is that people in the community could do the same thing or even develop new methods to better interpret RNAi screen data," Martin added.
Life Tech's willingness to open up its siRNA sequence data has already been seen in a recent Nature publication in which NCATS researchers reported the identification of a number of genetic regulators of parkin — a gene closely associated with Parkinson's disease — through a genome-wide RNAi screen using the company's siRNAs.
Martin said that the institute aims to continue down this road, not only including full sequence information for all siRNAs used in its screens, but also depositing the data into PubChem.
At the same time, he said that he hopes other siRNA vendors will follow Life Tech's lead.
"Libraries have been around for almost a decade, and the status quo has been that [vendors] will allow you to publish a fraction of the sequences along with the screen or a paper, but definitely not the full library or even close to that," he explained. "Maybe there will be a push [to lift such restrictions] from other groups … and maybe some of the journals will begin to require more sequence deposition into the public space."
According to Nitin Puri, senior product manager of RNAi at Life Tech, the firm's decision was driven by the realization that "complete data transparency is critical for lead identification in genome-wide RNAi projects," and that there have been "multiple published screens to identify genes in the same biological process with little to no overlap in the resultant hits."
“Translation of siRNA library screening results into impactful downstream experiments is the ultimate goal of scientists using our library,” Alan Sachs, Life Tech's head of global research and development and the former vice president of Merck Research Labs, said in a statement. “The availability of these sequence data should greatly facilitate this effort because scientists no longer will be blinded to the actual sequence they are targeting.”
"We believe that this is a right step forward in making the screening-to-validation workflow easier for our customers and will also drive greater adoption of the Silencer Select technology," Puri added.