The National Institute of Environmental Health Sciences said last week that it has launched a 3-year project to develop a library of siRNA sequences targeting a number of human genes believed to be associated with environmentally related diseases.
The project, being conducted by the Translational Genomics Institute with the help of Icoria, is the first phase of a broader effort to develop an RNAi resource for the members of the NIEHS’s National Center for Toxicogenomics.
According to Ray Tennant, director of the NCT and head of the NIEHS’ RNAi initiative, the center’s microarray group collaborates with scientists from five institutions with the goal of bringing “definition to the field of toxicogenomics, which we view as the interface between science and [the] adverse effects of chemicals, … drugs, … and environmental influences.”
The groups, which work with each other as the Toxicogenomics Research Consortium, aim to identify biomarkers that would allow researchers to predict adverse effects, rather than simply respond to them once they happen, he told RNAi News this week. We want to “make what has primarily been an empirical science into a much more analytical effort,” Tennant said.
The institutions affiliated with the TRC include the University of North Carolina at Chapel Hill; the Fred Hutchinson Cancer Research Center; the Oregon Health and Science University; Duke University; and the Massachusetts Institute of Technology.
Over its roughly 3-year life, the TRC has relied heavily on gene-expression data gathered through microarray analysis, Tennant said. “One can identify putative novel genes or biological processes that may be involved in adverse effects using microarray analysis, but the … gap … between the [identification] and association in [determining] a causal relationship can be at times … very wide,” he explained.
“That’s where the RNAi project comes into play,” he said. “It is one of the functional [technologies] we are trying to use to make a link between the data obtained from microarray analysis and potential causal relationships to adverse phenotypes that may be induced by chemical or environmental stressors. [The RNAi initiative’s goal] is to give [us] … another tool in the toolbox to take the science forward.”
The first steps toward the development of the siRNA sequence library are being overseen by Icoria, formerly known as Paradigm Genetics, under a $3 million research contract granted by NCT, Tennant said.
Peter Johnson, chief business officer and chief medical officer at Icoria, told RNAi News that his company’s receipt of the RNAi library contract was a direct outgrowth of an existing relationship between the parties; under a five-year deal signed in October 2002, Icoria uses its gene-expression profiling technology to conduct toxicogenomics research for the NIEHS and NCT.
“We have had a long-standing relationship with the NIH … where we’ve been providing them gene expression microarray services and, periodically, other services as well,” he said. “One of the things they needed us to do here was to manage a project where specific RNAi products can be created to test the importance of environmentally sensitive genes.”
Tennant said that the individual consortium members “identified specific gene targets that they would be interested in having an RNAi tool for.” The result is an initial list of 75 genes, including ones associated with cancer, neurodegenerative diseases, neurotoxicity, and immunotoxicity, he said.
TGen, under the direction of Icoria, will develop siRNAs that target these genes, Tennant said. The NCT and TGen will then conduct tests, initially in HeLa cells, to ensure the siRNAs are functional. Validated sequences will be entered into the NCT’s RNAi library for use by its researchers.
According to Johnson, Icoria is “essentially … a contractor of the NIEHS, so we work with TGen to fulfill the stipulations of the [RNAi] contract.”
Richard Paules, the toxicogenomics facilitator for the NCT and director of the center’s microarray group, told RNAi News that the NCT is having the library put together in order to make life a little bit easier for researchers wanting to incorporate RNAi into their work.
“We will be … doing the initial work for our investigators who are interested in environmental health sciences so that they don’t have to validate, optimize, and do all the initial work to have functional knockdown,” he said.
Paules noted, however, that the NCT will not be providing actual RNAi oligos to the researchers. “We don’t want to compete with the private sector,” he said. “We’re disseminating this information, and [researchers] are welcome to get the oligos from whichever commercial vendor they like.”
Tennant said that the gene list is expected to grow as the project advances, although the finally tally remains uncertain. “Everything is done sort of incrementally, and our first effort here is to test the system out — how effective are these design constructs? How effective are they in actually targeting the genes that are [first] identified? And can we measure inhibition of these specific genes based upon these constructs? If that works out with the first 75 grouping, we will move on to more targets,” he said.
Paules also noted that while the RNAi initiative is currently focused on sequences targeting human genes, the project’s members are also considering expanding into rodent systems.
“We’ve also discussed creating stable hairpin structures,” he added. However, “that is much more involved, and we really think that right now the best use of our resources is to generate a broad spectrum of environmentally relevant siRNA oligo [sequences] that are validated and would be useful for our investigators.”
Tennant said that the sequences are ultimately to be made publicly available through the NCT’s Chemical Effects in Biological Systems database, a collection of information and resources related to the biological effects of chemicals and other agents that is currently under construction.
“This knowledge base … will house microarray and proteomics data linked to specific drugs, environmental stressors, chemicals, and specific adverse effects,” Tennant said. Data from RNAi initiative “will just be another component of this knowledge base that the scientific community will be able to access.”
Tennant said that the NCT expects to make the CEBS database available to the public in mid-2005. “As soon as we have accomplished that, the specific siRNA data file will be appended to the CEBS database,” he said.
— DM