NIH Common Fund Support for the Development of Protein Capture Reagents and Technologies
Production of Affinity Reagents for Human Transcription Factors
This initiative was aimed at producing an affinity reagent resource for human transcription factors of the broadest possible utility, with a high priority for the use of the reagents in chromatin immunoprecipitation (ChIP) studies. The Protein Capture program supported two awards in this area. See the original Funding Opportunity Announcement for more information about this initiative and ProteinCapture.org for the reagents that are currently available.
Drs. Seth Blackshaw and Heng Zhu at Johns Hopkins University implemented a production center with a highly efficient and cost-effective monoclonal antibody pipeline to produce protein capture reagents recognizing approximately 1,500-1,700 human transcription factors. The reagents produced by this group are distributed at a minimal cost by the Developmental Studies Hybridoma Bank, ensuring broad availability and wide accessibility. View Funded Research Information
Dr. Anthony Kossiakoff at the University of Chicago established the Recombinant Antibody Network (RAN). RAN is a collaborative, international, tri-center partnership with the main goal of generating customized recombinant protein capture reagents to all human transcription factors. Recombinant antibodies have many advantages when compared to the typical hybridoma technology for producing monoclonal antibodies. For example, no animals are used in the production process, and the modification of recombinant antibodies for broader applicability is relatively simple. View Funded Research Information
Technology Development for New Affinity Reagents against the Human Proteome
This initiative addressed a central challenge in the field. While a number of approaches for generating protein affinity reagents exist, the cost and throughput of current technologies represent significant roadblocks to the development of a comprehensive and broadly available resource of renewable affinity reagents to all human proteins. The development of a robust pipeline that goes from the selection of protein targets to the validation of the produced reagents is greatly needed. This Protein Capture program supported four awards that aimed to develop and/or improve approaches for obtaining renewable protein affinity reagents at high throughput and low cost. See the original Funding Opportunity Announcement for more information about this initiative.
Dr. Andrew Bradbury at Los Alamos National Laboratory, together with an outstanding team of international scientists that include Drs. Aled Edwards, Mathias Uhlen, Lund-Johansen, Daniele Sblattero, and Janet Oliver worked toward establishing a pilot, high-throughput, three-tiered antibody selection pipeline that involves yeast and phage display technologies. This approach could potentially increase throughput by ~100 fold compared to the selection and characterization of traditional monoclonal antibodies against each target, resulting in a dramatic reduction in costs. In most cases the result would be renewable polyclonal antibodies but monoclonal antibodies could also be developed when necessary. View Funded Research Information
Dr. John Chaput and Dr. Joshua Labaer at Arizona State University, Tempe worked toward developing novel bivalent affinity reagents called NuPromers (Nucleic acid Protein avimer). NuPromers are produced via a novel technology that combines a rigid DNA scaffold with two peptides that have affinity against a specific protein target. They applied this technology toward creating a relatively inexpensive and high throughput pipeline. View Funded Research Information
Dr. Brian Kay at the University of Illinois at Chicago together with Dr. Andreas Pluckthun at the University of Zurich, and Dr. Michael Weiner at Illumina formed a research collaboration to improve screening and evaluation technologies currently used to generate affinity reagents. This group compared three types of recombinant protein scaffolds as affinity reagents (single-chain fragments of variable regions (scFv), ankyrin repeat proteins, and fibronectin type III monobodies) and two types of display technologies (phage and ribosomal) against the same set of human proteins and worked to optimize a pipeline for producing recombinant monoclonal antibodies. Furthermore, within this project, the method called Phage Emulsion, Secretion, and Capture (ESCape) underwent optimization. This is a novel and ground-breaking approach for selection in phage display, where the generation of an emulsion phase allows the compartmentalization of each phage with the antigen linked to beads. View Funded Research Information
Dr. Hyongsok Tom Soh at the University of California, Santa Barbara, collaborating with Dr. Lloyd Smith, Dr. James Thomson, and Dr. Ron Stewart at the University of Wisconsin, Madison, combined three technologies as follows: microfluidic selection, next-generation aptamer sequencing, and surface plasmon resonance (SPR) Imaging to warddeveloping a Quantitative Parallel Aptamer Selection System (QPASS) platform that should enable significant process improvements and cost reductions in aptamer generation, reducing the typical eight-ten rounds of aptamer selection to only three. Aptamer technologies also have the main advantage that once an appropriate reagent is generated it can be easily reproduced and distributed at very low cost. View Funded Research Information