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

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.