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288 Development of Alternative Affinity Capture Reagents for Cancer Proteomics Research
Number of anticipated awards: 3
(Fast-Track proposals will be accepted.)
Budget (total costs): Phase I: $150,000;
Phase II: $750,000
(Note: It is strongly suggested that Proposals adhere to the above budget amounts. Proposals with budgets exceeding the above amounts may not be funded. Phase I project periods may last a maximum of 9 months.)
The deadline for receipt of all contract proposals submitted in response to this solicitation is: November 9, 2009.
Summary:
Thousands of antibodies are produced every year by commercial companies. However, many of these antibodies are known to be poorly characterized and suboptimal across multiple applications. Polyclonal antibodies lack the reproducibility of monoclonal antibodies. Likewise, the production of monoclonal antibodies is expensive and may months to produce. Even after production, a monoclonal antibody may not be specific for the target of interest, may not work in the needed assay, or could not be used in combination with other antibodies due to an antibody's large size and subsequent competition for overlapping binding domains. As such, the high costs associated with producing even small quantities of monoclonal antibodies represent a large barrier towards cost-effective reagents and resources for proteomic technology research and clinical adaptation. The goal of this project is to develop reproducible, highly qualified/characterized alternative protein capture reagents for the cancer research community. The development of these affinity capture reagents will be done in coordination with NCI's Clinical Proteomic Technologies for Cancer (CPTC) and be targeted to a list of over 100 purified recombinant proteins being constructed and characterized through this initiative. There is a strong support for the development of renewable, alternative capture reagents that could be produced more efficiently and cost-effectively than monoclonal antibodies and hence, provide an inexpensive, well-characterized resource for the scientific community. Several technologies such as yeast single chain antibodies, or synthetically produced capture reagents such as aptamers, peptide aptamers, synbodies, and nanotechnology reagents demonstrate a potential for alternative, reproducible, cost-effective reagents in proteomics research.
Project Goals:
The goal of this project is to develop alternative affinity capture reagents that can effectively compete against ELISA-based antibody technologies in terms of protein recognition, binding affinity, and detection and can be reproducibly produced in a cost-effective and efficient manner. These affinity reagents will ultimately be designed to target proteins developed in coordination with the Clinical Proteomic Technologies for Cancer that is producing purified cancer-related proteins for research programs. Furthermore, these capture reagents must pass performance characterization criteria and be made available as a resource to the scientific community. The suggested choices of performance platforms the affinity reagents must be required to surpass include ELISA-based assays, Mass spectrometry-based quantitative assays, Western blot, immunohistochemistry, and immunoprecipitation. In addition, other considerations include quantitative information for affinity reagents (Kd, on-rate, off-rate), the actual binding epitope in order to interpret the quantitative characterization, and application in multiplex platforms such as microarrays. While it is expected that initial development and quality assurance/quality control costs may be comparable to that of monoclonal antibodies, it is intended that production costs of these renewable reagents will be significantly lower.
During the phases I and II, offerors are encouraged to coordinate and pursue selected antigen targets in the following reference: Malu Polanski and N. Leigh Anderson. (2006) "A List of Candidate Cancer Biomarkers for Targeted Proteomics." Biomarker Insights 2:1-48.
- Work with the Clinical Proteomic Technologies for Cancer community (http://proteomics.cancer.gov), private and public sectors to identify appropriate minimum characterization criteria/validation assays (Commercially available ELISA kits can serve as appropriate tests for performance criteria).
- In coordination with Clinical Proteomic Technologies for Cancer program staff, select and generate affinity reagents to at least ten protein targets and demonstrate equivalent or improved performance to ELISA and other affinity-based platforms.
- Present findings to an NCI CPTC Evaluation Panel and demonstrate how the capture reagents compare in binding affinity to antibody-based platforms such as ELISA and have improved cost effectiveness and throughput capabilities in production compared to antibodies.
- Research should be proposed with quantitative feasibility milestones.
Phase II activities and expected deliverables:
- Implement strategy and project plan for a fully functional affinity reagent development platform for at least 75 protein targets developed through CPTC. The reagents should be able to capture the target of interest from complex biological mixtures such as blood, plasma, or tissue.
- Test performance criteria against ELISA and other affinity platforms.
- Work with CPTC to integrate capture reagents into the proteomic research platforms.
