Actigenics, a six-month-old spin-off from France’s Centre National de Recherche Scientifique, is banking on the recent rise of interest in non-coding RNA — along with its early entry into the market — to drive its marketing strategy over the coming year.
Based in Ramonville, a suburb of Paris, Actigenics just launched its first product, a database of non-coding RNAs called Human RNAgate. The 10-person company is “just starting commercial activity,” according to Jean-Francois Chauvet, business development manager for the company. Nevertheless, he said, Actigenics has already signed several deals with pharmaceutical companies. “The growth is very quick because there is almost no competition in the market,” he said, “so we have the chance to be the first in this niche market at the moment.”
RNAgate includes more than 5,000 novel non-coding RNAs, according to David Vilanova, R&D manager for the company. He said that Actigenics has developed an in silico discovery pipeline that predicts non-coding RNA genes by identifying conserved regions between the human and mouse genomes. The Actigenics bioinformatics team then identifies non-coding RNA genes by mapping the conserved regions to Ensembl and eliminating those regions that Ensembl identifies as protein-coding genes. That set is narrowed down using a computational approach based on the unique secondary structures of non-coding RNAs, Vilanova said.
“That’s what we’re looking for conserved secondary structures,” he said. “Then we identify non-coding RNA genes, and we classify them into families based on this knowledge.”
Vilanova said the company has validated its in silico approach by comparing its results to published research on non-coding RNAs, and has determined that it performs at around a 90-percent accuracy level. Actigenics plans to validate the predicted non-coding RNA genes experimentally as well, but Vilanova noted that these genes are difficult to capture in the wet lab.
“The reason that we started with a bioinformatics approach is because most of these non-coding RNA genes have not been isolated by experimental procedures,” he said, citing the fact that they can be expressed in different tissues at different times, and their lack of a poly A tail — by which most of the mRNAs are isolated — as the primary obstacles to wet lab verification.
Although it may not face competition from the commercial sector, Actigenics does face the familiar challenge for bioinformatics data providers of publicly available data.
Vilanova cited Rfam at the Sanger Center, which focuses on microRNAs, a database of snoRNAs (small nucleolar RNAs) from Sean Eddy’s lab at Washington University, and the Database of Noncoding RNAs at Poland’s University of Poznan as some examples. However, he said, these public resources tend to focus on specific types of non-coding RNAs, and don’t provide “as exhaustive and complete of a database for non-coding RNA as the one we propose.”
In addition, Vilanova said, RNAgate provides information about the genes, proteins, and mRNAs that interact with the non-coding RNAs.
“The idea is not just selling a database, because biology doesn’t really need more data, it needs more knowledge to reduce the biological complexity,” said Chauvet. “We think that by adding the non-coding RNA layer we can reduce that biological complexity, because it’s a missing layer. It’s happening in the cells all the time and people are just ignoring it.”
Chauvet said that in addition to the database, Actigenics plans to offer bioinformatics services for customers interested in gaining additional knowledge about non-coding RNAs for specific genes, pathways, or diseases. The company also has a microarray design service called RiboSpot, for which it designs non-coding microarrays to study the behavior of specific pathways or the expression of microRNAs, snoRNAs, or shRNAs.
The microarray product will be one of the drivers for the company’s financial activities in 2005, Chauvet said. Actigenics has been funded primarily by grants so far, but will seek VC financing in the coming year, he said.
“We have reached a reasonable size now, we have a product, and we can also develop customized services, and next year will certainly be the right time to raise new funds to invest even more in R&D, particularly for the chips,” he said. “It’s an area where we want to invest because we can then provide not only information or customized services, but also a diagnostic tool.”