Epitope Mapping

Team: Ji Qiu, Ph.D, Karen Anderson, Ph.D., and Benjamin Katchman, Ph.D.

Antibodies are effective tools for biomedical research, disease diagnosis and therapeutics. A thorough understanding of the epitopes antibodies target will improve their utility as research, diagnostic and therapeutic tools.

Antibodies can be made by immunizing animals with inactivated toxin, bacterial or viral antigens. In the case of bacterial and viral antigens, the entire microorganism is used to immunize the animal. This often produces a robust humoral immune response to immunodominant antigens on the microorganism that can be harnessed to generate either polyclonal or monoclonal antibodies. A major obstacle in using these reagents is identifying the epitope that the antibody binds to on the microorganism. This limitation hampers developing improved affinity reagents and creates a vulnerability in the detection capability of the antibody, should the epitope no longer be present on a select agent. Therefore, a high throughput technology platform to identify protein antigens of antibodies would be highly desirable.

Our Antigen-Specific Epitope-Targeting (ASET) arrays will quickly and easily identify epitopes and enable rapid mapping antibody epitopes at the amino-acid level. Our approach will bypass the expensive cost of synthetic peptides, challenges of antigen purification, and the uncertainty of random peptide library screening. A nested series of deletion mutants, N-terminal (NDM), C-terminal (CDM), internal (IDM) and tiling peptides can be generated rapidly and screened on ASET arrays at a low cost. Hundreds of arrays can be produced in one preparation and used for screening for many different antibodies to the target antigens. Our ASET arrays will allow epitope mapping in physiological buffers or under denaturing conditions. One previous example of this was mapping the epitope location for a known antibody/epitope combination of p53 (see figure, work of Rodrigo Barderas, Ph.D. currently faculty at University of Madrid).