By Doug Macron
As it enters its final year, Europe's SIROCCO, a consortium of RNAi and microRNA researchers focused on RNA silencing, has added three new members to lend the initiative additional expertise in bioinformtics and therapeutics, Gene Silencing News has learned.
According to Aileen Hogan, SIROCCO's project manager, the initiative had set aside about €1 million ($1.3 million) of the money it received when it was established in anticipation of adding new members near the end of its run. The new members bring the total number of participating organizations to 28.
About a year ago, it announced that it wanted to use that money to add new members with know-how in computational analysis and modeling, and who could help advance discoveries made by other consortium members toward diagnostic and clinical applications (GSN 10/29/2009).
On the bioinformatics side, SIROCCO ultimately decided to add two new members: the European Bioinformatics Institute, a Hinxton, UK-based branch of the European Molecular Biology Laboratory.
Heading up the SIROCCO work there is Anton Enright, whose research focuses on predicting and describing "the functions of genes, proteins, and in particular regulatory RNAs, and their interactions in living organisms," according to his lab website. "We are also interested in analysis of biological networks, protein-protein interactions, clustering algorithms, and vitalization techniques."
The other new bioinformatics partner is Estonia-based data-management firm Quretec. Although the company does not exclusively focus on biological data, it does have a bioinformatics unit that it describes as a joint effort with the department of computer science at the University of Tartu and the government-funded Estonian Biocenter.
The bioinformatics group's specific focuses include gene regulation, gene-expression data analysis, biological data mining, systems biology, combinatorial pattern matching, and biomedical research database software, according to Quretec.
Hogan said that although there are existing SIROCCO members with bioinformatics capabilities, they tend to focus on their own projects and interests. "Our responsibility was to try to bring [all the data generated by consortium members] together," she said.
Hogan noted that in many cases, SIROCCO researchers think that their datasets wouldn't be of interest to other members because they are too limited.
But this is not the case, she said. "Small [datasets] are interesting biologically, as well. When you do some microarrays or relatively small [experiments], you don't need massive high-throughput sequencing to be interesting. The idea was to try to get all these data together and look for new patterns, and also to help consortium members with their searching."
For instance, Hogan recalled a talk during SIROCCO's annual meeting in Heidelberg in October on Huntington's disease given by members from the University of Barcelona. Consortium member David Baulcombe "piped up and said, 'This reminds me of a phenomenon in maize called paramutation.' So by working from corn right through to humans, we might see something interesting come up," she said.
Together, Quretec and EBI will centralize SIROCCO datasets "so that they are accessible and searchable," initially for consortium members but ultimately for the general scientific community, Hogan added.
When it comes to taking advantage of SIROCCO research for therapeutic applications, the consortium has brought on board Markus Stoffel, a researcher at the Swiss Federal Institute of Technology Zurich who specializes in the "molecular and genetic mechanisms that regulate glucose and lipid homeostasis and that are dysregulated in complex human diseases including type II diabetes," according to the institute.
Previously a researcher at Rockefeller University, Stoffel is also a member of Alnylam Pharmaceuticals' scientific advisory board and has conducted research examining the roles of microRNAs in disease.
Hogan said that, as part of SIROCCO, he will study different ways to chemically modify small RNAs to improve their stability in vivo using animal models of various diseases, initially diabetes, with an eye toward advancing them as therapeutics.
SIROCCO, short for Silencing RNAs: Organizers and Coordinators of Complexity in Eukaryotic Organisms, was established in January 2007 with €11.8 million ($17.5 million) in funding from the European Union (GSN 4/26/2007).
The consortium’s primary goals are to “characterize the full complement” of miRNAs and siRNAs in animals and plants using bioinformatics, genomics, biochemistry, cell biology, and genetics.
The group's researchers study miRNA and siRNA profiles "that are associated with development, disease, and phenotypic divergence within populations," according to SIROCCO. Consortium deliverables include "databases of silencing RNA sequence and function in several organisms, new technologies for detection and manipulation of these RNAs, and information that will allow small RNA profiles to be used as molecular markers and diagnostic tools.
"SIROCCO will analyze the components of the small RNA silencing systems in order to identify potential targets for disease therapy and to improve the specificity with which therapeutic agents are used," the consortium said.
The consortium is set to run until Sept. 30, 2011, and while the members have produced "wonderful research," it won't be extended, Hogan said.
Still, the European Commission routinely issues calls for proposals and it is possible that different projects handled by SIROCCO could receive new funding, she noted. At the same time, many relationships forged between members are expected to last.
"We sent money to people to have lab exchanges … [which] developed lines of communication" that otherwise might not have been established, Hogan said. "I think that those will … continue."
SIROCCO is holding its final annual conference in September next year.
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