Study Suggests Prevalence of Off-Target Effects in Drosophila Screens
Researchers published this week data suggesting that off-target effects may be more prevalent in Drosophila RNAi screens incorporating long double-stranded RNA than previously thought.
The findings were published in the online version of Nature by Philip Beachy and colleagues at the Johns Hopkins University School of Medicine.
According to the Nature paper, “the use of long double-stranded RNAs in Drosophila, where Dicer-mediated processing produces small RNAs inside cells, has been thought to reduce the probability of … off-target effects.”
However, using a genome-wide RNAi screen for novel components of Wingless signal transduction17 in Drosophila S2R1 cells, the researchers found “few, if any legitimate candidates. Rather, many of the top candidates exert their effects on Wg response through OTEs on known pathway components or through promiscuous OTEs produced by tandem trinucleotide repeats present in many dsRNAs and genes,” they wrote.
“Genes containing such repeats are overrepresented in candidate lists from published screens, suggesting that they represent a common class of false positives,” they added.
To deal with the issue of OTEs, Beachy and colleagues proposed a few measures that could be taken to “produce more reliable lists of candidates” in RNAi screens using long dsRNAs.
“First, libraries should be designed to avoid sequences present in multiple genes, thus preventing the identification of false positives through promiscuous OTEs,” they suggested. “Second, phenotypic effects should be confirmed with more than one non-overlapping dsRNA for each candidate identified. Such testing with multiple dsRNAs would also have the benefit of reducing false positives that can arise due to noise inherent in screens of large numbers of items.”
They added that “RNAi-based screens at best merely provide a starting point in the identification and further mechanistic study of genetic elements with roles in a biological process of interest.”
Atugen RNAi Drug Shows Efficacy in Pancreatic Cancer Model
SR Pharma said this week that its subsidiary Atugen has demonstrated therapeutic efficacy of its lead RNAi drug candidate, Atu027, in animal models of pancreatic cancer.
According to the company, the data showed inhibition of both cancer growth and the prevention of metastatic spread, with no adverse effects.
SR Pharma said the data support the development of Atu027 for pancreatic cancer. The company said phase I testing is expected to begin next year.
Exiqon Establishes US Sales Facilities in Massachusetts
Exiqon said this week that it has established a sales, distribution, and technical support facility in Woburn, Mass.
The establishment of a US presence, Exiqon said, allows the company to target US customers while allowing its existing Danish facility to focus on sales opportunities in Europe and Asia, where a distributor network is being put together.
Protiva Takes Inex Dispute to US with California Lawsuit
Protiva Biotherapeutics said last week that it has filed a lawsuit against one-time parent firm Inex in the Superior Court of the State of California.
The suit builds upon an earlier suit Protiva filed against Inex in Canada (see RNAi News, 3/30/2006). The companies are currently disputing the ownership of an oligo delivery technology as defined by 2001 agreements that led to the spin out of Protiva from Inex.
According to Protiva, the latest lawsuit alleges, among other things, that Inex intentionally interfered with a licensing deal between Protiva and Sirna Therapeutics. Protiva and Sirna are also engaged in litigation regarding the delivery technology.
The suit is seeking general, specific, and punitive damages, Protiva added.
This week, Inex issued a statement saying that it is aware of the new lawsuit.
"We believe the Protiva claims have no merit and we are confident of our contractual and intellectual property rights under our 2001 agreements that created Protiva,” Inex President and CEO Timothy Ruane said in the statement. “The license granted to Protiva is very specific and does not include the delivery of oligonucleotides, including siRNA."
Asuragen Announces Participation in FDA’s MQCC
Asuragen said this week that it was an Affymetrix test site for the US Food and Drug Administration’s Microarray Quality Control Consortium — a community-wide effort to evaluate the reliability of DNA microarray data.
The MAQC involves 137 participants representing 51 organizations, including the National Institutes of Health, the US Department of Agriculture, and the Environmental Protection Agency. Results from the effort, which determined that microarray data from different platforms can be “reproducible and comparable,” were published in a series of articles in last Friday’s issue of Nature Biotechnology.
Cyntellect Receives CE Mark for LEAP System
Cyntellect said last week that it has gained the European Union’s CE mark for its Laser-Enabled Analysis and Processing system.
The company said that it has also shipped a LEAP system to “a major pharmaceutical company customer in Europe,” marking the first commercial delivery of the system to the EU.
"CE marking of LEAP represents a major commercial milestone for Cyntellect and opens up an important market for our products," said Fred Koller, Cyntellect's president and CTO, in a statement.
LEAP is an automated instrument that combines optical imaging of cells, real-time image analysis, and high-speed laser manipulation of live cells in microplate formats. Cyntellect has developed the platform for a number of applications, including siRNA transfection.