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Phage-DMS: a comprehensive method for fine mapping of antibody epitopes

By Meghan E Garrett, Hannah L Itell, Katharine H.D. Crawford, Ryan Basom, Jesse Bloom, Julie Overbaugh

Posted 13 May 2020
bioRxiv DOI: 10.1101/2020.05.11.089342 (published DOI: 10.1016/j.isci.2020.101622)

Understanding the antibody response is critical to developing vaccine and antibody−based therapies and has inspired the recent development of new methods to isolate antibodies. However, methods to define the antibody-antigen interactions that determine specificity or allow escape have not kept pace. We developed Phage−DMS, a method which combines two powerful approaches − immunoprecipitation of phage peptide libraries and deep mutational scanning (DMS) − to enable high−throughput fine mapping of antibody epitopes. As an example, we designed sequences encoding all possible amino acid variants of HIV Envelope to create phage display libraries. Using Phage-DMS, we identified sites of escape predicted using other approaches for four well characterized HIV monoclonal antibodies with known linear epitopes. In some cases, the results of Phage−DMS refined the epitope beyond what was determined in previous studies. This method has the potential to rapidly and comprehensively screen many antibodies in a single experiment to define sites essential for binding to antigen. ### Competing Interest Statement Julie Overbaugh and Meghan Garrett are co-inventors on a patent describing the Phage−DMS method. The patent applicant is Fred Hutchinson Cancer Research Center. The patent is pending, with the patent application number PCT /US2020/020429. The patent describes Phage−DMS as a method of mapping antibody epitopes and determining changes in residues of a protein that abolish binding of the protein to a candidate binding molecule.

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