The Accelerated Molecular Probe Pipeline (AMPP)

The generation of molecular probes (usually monoclonal antibodies) remains a critical bottleneck in biomedical research, biomarker discovery, and diagnostic test development. Several approaches have been developed to overcome this problem. For example, yeast display libraries express diverse single chain-fragment variable (scFv) antibodies on the surfaces of Saccharomyces cerevisiae cells. By using fluorescent-activated cell sorting (FACS), yeast clones that bind specifically to antigens can be selected from naïve libraries in 2 to 3 weeks. Unfortunately, selected probes that perform well on yeast cell surfaces rarely perform well in solution. Because of such issues, monoclonal antibody generation remains a critical rate-limiting step in biomarker discovery and diagnostic test development.

In order to improve the speed and throughput of molecular probe development, the Cangelosi lab at Seattle BioMed has initiated a project entitled the Accelerated Molecular Probe Pipeline. The AMPP project is a collaboration between Seattle BioMed and the University of Queensland, University of Virginia, PATH, and the International Centre for Diarrheal Disease Research, Bangladesh.

The AMPP utilizes strategies that leverage the speed and throughput of yeast scFv display, while overcoming its innate limitations. Mass spectroscopy- and FACS-based methods employ yeast-displayed scFv as molecular probes, without requiring scFv functionality in solution. Novel nanoparticle scaffolds are used to improve the functional affinity of scFv binding to antigens. As a model for the development of these approaches, the AMPP is being used to identify novel cyst antigens of Entamoaeba histolytica, an important enteric pathogen in the developing world. The AMPP will be applied first to identify and validate these biomarkers, and then to generate high-activity scFv probes for incorporation into an improved point-of-care diagnostic test for E. histolytica cysts in patient stool.

If successful, the AMPP will change the way molecular probes are generated for research, biomarker discovery, and diagnostic testing. It could benefit any research and development effort that utilizes molecular probes, and pave faster routes to new vaccines, drugs, and diagnostics.