P R O T EO M ICS P R O J EC T S
HAI brings antibody researchers together
ies per human protein would be ideal because many detection assays such as Antibodies are tools that are easy to ELISAs require two antibodies. In adtake for granted—until you realize that dition, multiple antibodies would help antibodies to your favorite protein(s) scientists confirm results. “The number do not exist. As more large-scale, highone problem with antibodies is concern throughput proteomics projects are about cross-reactivity with related conducted, it is becoming obvious that epitopes, and having two antibodies antibodies against only a few popular against different epitopes of the same proteins are available from commercial protein is about as confirmatory as you or academic sources. The lack of antican get,” he says. bodies “is clearly a huge bottleThe second goal of HAI is to neck for researchers in general establish a database that would because when you find a protein list all of these renewable reof interest, almost always the first agents. With funding from the EU thing you want to do is get more ProteomeBinders project, Uhlén information about it, and almost has created a draft version of such all the characterization steps a portal, called Antibodypedia, require having some sort of affinwhich he presented to HAI workity reagent,” says Michael Snyder, shop attendees at the HUPO Sixth who is at Yale University and is a Annual World Congress in Seoul co-chair of HUPO’s Human Antilast fall. “Our hope is that it will be body Initiative (HAI). a little bit like Wikipedia, where To address this growing probthe community provides inforlem, the HUPO Council decided mation, but this is still quite an to start HAI in 2005. At that time, experiment,” says Uhlén. Mathias Uhlén (a co-chair of Instead of a physical collecHAI) and co-workers at the Royal tion of affinity-reagent aliquots, Institute of Technology (Sweden) Antibodypedia will be a virtual and several other institutions resource that will include detailed worldwide were creating a large information about these tools. Antibodies, wonderful antibodies. Confocal image of huresource called the Human Pro“We will score antibodies accordman cells. An HPA-generated antibody stains a mitochondritein Atlas (HPA). In an example ing to how much validation is al protein called hTom22 (green). The cytoskeleton (red) and nuclei (blue) also are visible. of good timing, HPA became the provided, and we will also enable first project endorsed by HAI, and the community to discuss results the first version of the atlas was they have obtained with these unveiled at the HUPO Fourth Annual Although HPA is the most visible antibodies,” he explains. This is an imWorld Congress in 2005 in Munich. project promoted by HAI, it is not the portant feature “because at least in our Because HUPO is not a funding body, sole focus of the initiative. According to hands, two-thirds of the commercial members of the initiatives must obtain Snyder, HAI has three main objectives. antibodies do not work,” he reports. grants on their own. Unlike other First, HAI encourages researchers to Thus, a lot of time and money is wasted HUPO initiatives such as the Plasma generate antibodies. HPA falls under because such information is not easily Proteome Project or the Human Brain this mission, because many antibodshared among researchers. Also, scienProteome Project, however, HAI has ies are being generated by this project, tists often complain that some companot initiated projects on specific topics. and several aliquots are available to nies are unwilling to provide validation Instead, the group holds workshops researchers who wish to collaborate data for their antibodies, so this issue to obtain community feedback and to with Uhlén’s group. However, these could pose a problem for the database. bring together leaders in the field. As a antibodies are polyclonals, so limited “One of the reasons we would like result of some of these discussions, HAI amounts exist. Workshop participants to start this Antibodypedia is because endorses certain projects, such as HPA, from around the world have agreed that with this resource, it will be very clear that are consistent with its vision, says renewable affinity reagents are neceswho provides validation data, and they Uhlén. sary, so HAI is starting to encourage the will be scored,” says Uhlén. Therefore, HPA is an image repository that development of monoclonal antibodies if a visitor to the database sees that two shows the expression levels of various and antibody mimetics, such as novel companies provide antibodies against human proteins in 700 normal and canprotein scaffolds, explains Peter Hudthe same protein, he or she might prefer cerous tissues and cell lines, says Uhlén. son, who is with the Commonwealth to get the antibody from the company HPA researchers generate ~120 proteins Scientific and Industrial Research that has uploaded a western blot or IHC every week that are then injected into Organisation (Australia) and is another image that demonstrates the reagent’s animals. The resulting antisera are afHAI co-chair. performance. Another benefit of Antifinity-purified, and the antibodies are Snyder points out that two antibodbodypedia is that it should help investiMATHIAS UHLÉN
validated with protein arrays, western blots, and immunohistochemistry (IHC) assays. The project generates many new validated polyclonal antibodies every week, and these reagents are used to localize proteins in tissues and cell lines. Uhlén predicts that the atlas will continue to produce ~3000 antibodies every year and that a draft of the localization of every human protein will be ready by 2015.
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gators and companies figure out which proteins lack binders. Uhlén plans to release a pilot version of the portal this spring. Finally, the third objective of HAI is to develop standards for characterizing antibodies and for reporting these findings, says Snyder. Because antibodies can perform differently in different assays, the same criteria would not apply to all applications. Some HAI workshop attendees also participate in the HUPO
Proteomics Standards Initiative, so working groups have formed and topics are being discussed. However, no firm consensus has been reached with regard to antibody standards. HAI members may collaborate with other HUPO initiatives and endorse additional projects, but their efforts are limited by the amount of funding available. Snyder says this is a major challenge to progress in the field. “The problem is: funding agencies know this is an
important area and want to work on it, but very few have stepped up to take the lead,” he explains. Just as large consortia have been formed to sequence the genome and discover early-detection biomarkers, a large-scale effort to generate and characterize antibodies needs to be established, he points out. “We’ve been prodding to get that to happen, but I think only very modest forms” have been initiated, says Snyder. —Katie Cottingham
P EO P LE
New Editorial Advisory Board members Thomas P. Conrads is an associate professor of pharmacology, biomedical informatics, and medicine at the University of Pittsburgh School of Medicine and co-directs the Clinical Proteomics Facility in the University of Pittsburgh Cancer Institute. He obtained his Ph.D. in biochemistry at Ohio State University and completed postdoctoral training at Pacific Northwest National Laboratory. His research program focuses on the development of new chemistry and biology technologies for the characterization of proteomic and metabolomic changes that are associated with clinically relevant questions in cancer biology. The goal of these efforts is to enhance the management of patients with cancer through improved early detection, patient stratification, and monitoring for therapeutic efficacy, outcome, and recurrence. Brian Haab is a senior scientific investigator and director of the Laboratory of Cancer Immunodiagnostics at the Van Andel Research Institute. He
holds a Ph.D. in chemistry from the University of California Berkeley and completed his postdoctoral training at Stanford University. Haab’s laboratory has developed several novel antibodyarray methods, including methods for high-sensitivity detection, low-volume and high-throughput sample processing, improved data analysis, probing glycan structures, and detecting protein–protein interactions. His team has identified several protein and glycan alterations in the blood of pancreatic cancer patients and is pursuing the further development and validation of disease markers and studies on the roles of specific tumor secretions in cancer progression.
are in the fields of crop proteomics, biochemistry, and molecular biology with a special focus on signal transduction in cells.
Setsuko Komat su is a labora tory head at the National Institute of Crop Science and is a professor at the University of Tsukuba (both in Japan). She ob tained her Ph.D. from Meiji Pharmaceutical University (Japan), and her dissertation focused on the role of protein kinase-dependent phosphorylation during mammalian fertilization. She was previously employed at Meiji Pharmaceutical University and then at the Keio University School of Medicine (Japan). In 1993, Komatsu was a senior researcher at the National Institute of Agrobiological Sciences. Since 1990, she has used protein sequencing and MS to study plant proteomics. Her main research interests
David M. Lub man is the Maude T. Lane Professor of Surgery and is a professor of pathology and chemistry at the University of Michigan (UM) Ann Arbor. He is also a member of the bioinformatics program and the Comprehensive Cancer Center at UM. He obtained his Ph.D. in physical chemistry in 1979 from Stanford University under the direction of Richard N. Zare and was a fellow at the Weizmann Institute of Science (Israel). Lubman’s laboratory uses liquid separations and protein microarrays for intact protein analysis. With these methods, the group studies changes in global phosphorylation and glycosylation patterns as disease markers, in addition to the autoantibody response in patient plasma. Recently, the laboratory has been developing techniques for microproteomics of cancer stem cells, mouse tissues, and protein pathways related to disease. Lubman also has been involved in technology development that has resulted in several small start-up companies. He is a Fellow of the American Association for the Advancement of Science. Biographies and photographs of other new Editorial Advisory Board members will appear in the February issue of JPR.
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