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Cenix, IMM Collaborate on RNAi Screen for Malaria-Related Genes; Eye Full Human Genome


Building on a recently completed pilot study, Cenix BioScience and the Instituto de Medicina Molecular in Portugal are collaborating to identify human genes necessary for the malaria infection process, the groups said last week.

According to the partners, the effort is initially focused on more than 800 genes, but may be expanded to the entire human genome should IMM be able to secure sufficient funding. Should it do so, IMM hopes that Cenix's technology will allow it to identify the best targets for new malaria treatments.

Under the terms of the arrangement, Cenix will be paid undisclosed fees to use its high-throughput RNAi technology to screen genes identified by IMM researcher Maria Mota. Cenix CEO and CSO Chris Echeverri told RNAi News this week that IMM would own all results derived from the effort.

Mota has been working on malaria for almost a decade and has developed an in vitro assay system designed to track the process of sporozoite infection by the parasite Plasmodium berghei ANKA in cultured human liver cells, she told RNAi News this week.

"I wanted to study the host response from the liver cell to the parasite," she said. "I thought, 'I need some sort of functional assay. I cannot have just a list of genes.' So I decided to design something applying siRNAs."

Mota said that her assay involves introducing sporozoites, obtained from the salivary glands of malaria-infected mosquitoes, into liver cells that have been transfected with different RNAi oligonucleotides. While this approach was successful, she said that it worked on far too small a scale to allow her "to look for other genes that are really important."

"I wanted to study the host response from the liver cell to the parasite. I thought, 'I need some sort of functional assay. I cannot have just a list of genes.' So I decided to design something applying siRNAs."

Mota said that she unsuccessfully investigated possible collaborations to scale up her assay with a number of companies before she was turned onto Cenix by a visiting researcher from the Max Planck Institutes, which along with the European Molecular Biology Laboratory, spun out Cenix 1999.

Mota said that when she was discussing her work with the Max Planck researcher "he said, 'I think Cenix is trying to develop these kinds of screens and I think they are well advanced.' It was this person that put me in contact with Cenix."

According to Echeverri, Mota first inquired about Cenix's services in early 2004.

"They had quite a nice assay," he said, but "they … didn't have the resources to build that up, or the know-how to do a high-throughput, genome-scale RNAi project themselves. So they asked us if we could help."

Echeverri noted that, like many academic researchers, Mota was uncertain whether her lab would be able to afford Cenix's services — something he called "a basic problem."

"The key way in which we've tried to get around this is to first do a very small, efficient, and cheap feasibility study, which makes it affordable," Echeverri explained. "We can test their assay and see if we can generate some feasibility data in a high-throughput RNAi format such that they can use that data … in a grant proposal and hopefully get funds [to] … subcontract the screening portion of the work to us. And that's exactly what happened."

As for how much a small study like this usually costs, Echeverri declined to provide specific numbers, noting that "it depends heavily on how much assay work the lab has done already." He did state, however, that "in some cases, we can help by polishing [the work] up and adapting [it], and we can do something below €10,000 ($11,946). But usually we'll try to make that feasibility study for an academic lab fit below €20,000."

It is not clear what Cenix typically charges non-academic customers for these services.

Echeverri said that the pilot work conducted with Mota's lab simply involved "looking at silencing results under the conditions that are required for the infection assay … and being able to show that we are able, with different genes, to get good silencing and, still under those conditions, get good detection of changes in infection rates. It was promising enough that we knew what we would need to do to get that to full 'screenibility.'"

With these data, as well as data from other research efforts, Mota said she was able to secure approximately €1.2 million from both the European Science Foundation and the Portuguese government. While these funds are supporting a number of different projects, Mota said that about €500,000 has been dedicated to her lab's work with Cenix.

"The funds we've gotten so far can cover" roughly 800 genes, Echeverri said. "Maria chose which genes to focus on initially, and she included all the kinases along with a few other genes that are of particular relevance for these pathways. The results are already starting to come in and there are some beautiful hits that are showing up."

Mota said that nearly all of the genes have been screened by now, but noted that it will be a few months before all of the follow-up work is completed. "I'm not so sure I'm not being too optimistic, but I would hope that by the end of this year or the beginning of next year we'll have this dataset complete," after which time the data will likely be published.

Echeverri pointed out that the project's timeline "is limited not by the throughput of analysis, but by the supply of sporozoites. Mosquitoes have to be manually dissected, and this is familiar territory for us since we manually dissected millions of worms to get through our genome-wide C. elegans screen" (see RNAi News, 4/1/2005).

"However, mosquito dissection … is very delicate — more delicate than what we've done with C. elegans in the past," he said. While there are several members of Mota's lab on site at Cenix handling the dissection work, it's still a laborious process and "the key bottleneck right now," according to Echeverri.

"The hope is that we can find further funding so that we don't stop at 800 [genes], and we can continue and go all the way through the whole genome … [as well as] train several of our people and make sure [dissection] is no longer the bottleneck," he said. "Then we'd be able to go through the genome quite fast."

"We'd love to enlarge [our work] to the whole genome," Mota said, adding that plans are underway to apply for additional funding that would support this effort. She also said that while she would be interested in possible commercial partnerships, no discussions have taken place with any possible industry partners.

— Doug Macron ([email protected])

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