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As the funding for the Biodefense Proteomics Research Centers (PRCs) comes to an end, a tidal wave of data and results is just starting to emerge. The National Institute of Allergy and Infectious Diseases (NIAID) has not renewed the basic science program for a second 5-year term, but the institute is making plans to keep the resources and data already generated by PRCs publicly available. In 2002, the NIAID broad agency announcement (BAA) for the PRC program asked researchers to propose new or conventional proteomics approaches for the study of biodefense, emerging, and re-emerging pathogens to identify candidate vaccine and therapeutic targets. “What interested me about the centers was the opportunity not only to do interesting proteomics but to develop technologies,” explains Josh LaBaer, who is the principal investigator of a PRC and is at the Harvard Institute of Proteomics (HIP). Since 2004, seven PRCs have been conducting proteomics studies on NIAID Category A, B, and C pathogens. For example, groups at Caprion Proteomics and the University of Montreal apply MS to study the biology of Brucella abortus and the host-cell response after infection with the bacterium. LaBaer’s group at HIP is generating large collections of clones that encode Bacillus anthracis and Vibrio cholerae genes, developing protein microarrays to study immune responses to these pathogens, and creating knockout strains to find essential genes and potential vaccine targets. A unique aspect of the PRC program is the establishment of the Resource Center for Biodefense Proteomics Research, which includes researchers at the Protein Information Resource (PIR) at Georgetown University Medical Center and the Virginia Bioinformatics Institute (VBI) who are responsible for the public dissemination of PRC data and reagents. The third partner is Social and Scientific Systems, a small business that maintains
10.1021/pr8005809
2008 American Chemical Society
the homepage for the program and coordinates conference calls and yearly meetings. With their own specialized bioinformatics infrastructures, PIR and VBI researchers collect, organize, and post all of the host–pathogen data for public viewing. PIR maintains the master list of proteins and reagents, whereas VBI hosts lists of protocols, technologies, and data. JOSH LABAER
NIAID Biodefense Proteomics Research Centers
Anthrax proteins. A portion of a selfassembling protein microarray is shown. Red spots indicate that B. anthracis proteins have assembled efficiently, and green and blue spots indicate reduced assembly efficiency.
Because of the Resource Center’s data integration efforts, researchers can mine and compare data across different experiments and organisms from various PRCs; Cathy Wu of PIR explains that this type of search could lead to the identification of potential targets that are not apparent from the data of any individual center alone. The initial hurdle for the Resource Center was to figure out how to integrate different data types from various centers that were applying disparate techniques. “Now, the main challenge is to cope with the volume of data, because these centers are just warming up!” says Wu. Just as PRCs are starting to churn out data, the program is set to expire. “It’s a shame that the program was discontinued after only the first round,
because these sorts of things take ∼10 years to mature and get to a point where you start to see fruit from the labor,” says LaBaer. “We spent the first 3 years laying a foundation, and now that the foundation is laid, the funding is no longer there.” According to Maureen Beanan of NIAID, the institute has no plans to issue another BAA for basic science proteomics proposals, but she says the institute is still interested in these types of projects. “When the PRC projects are completed next June, at the end of the planned 5-year project period, NIAID remains strongly committed to advancing the understanding of pathogen and host-cell proteomics through a variety of grant mechanisms, including investigator-initiated projects funded through the peer-reviewed grant process,” she says. Wu emphasizes that the data and resources generated by PRCs still will be publicly accessible after the close of the program. “In terms of the data that we are hosting in the Resource Center, I understand that they will be consolidated with [another NIAID project’s] data and presented in the future in some fashion by NIAID,” she explains. The look and feel of the new site may differ because the infrastructures at PIR and VBI cannot be replicated easily, and NIAID may have other ideas for the best way to present the data, adds Wu. For now, PRCs and the Resource Center still are in the thick of things, generating and posting data on pathogens and host cells. LaBaer notes that, overall, the PRC experience has been positive and has allowed his group to further develop various technologies, including proteome-scale protein microarrays. Wu says her team has learned a lot about handling various types of data, and she often is tapped by other organizations to discuss the centralized resource center concept. Until December 2009, the data and resources are freely available at www. proteomicsresource.org. —Katie Cottingham
Journal of Proteome Research • Vol. 7, No. 9, 2008 3641
