Phage-DMS: A Comprehensive Method for Fine Mapping of Antibody Epitopes
Meghan E. Garrett,
Hannah L. Itell,
Katharine H.D. Crawford,
Ryan Basom,
Jesse D. Bloom,
Julie Overbaugh
Affiliations
Meghan E. Garrett
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Hannah L. Itell
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Katharine H.D. Crawford
Divisions of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
Ryan Basom
Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Jesse D. Bloom
Divisions of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
Julie Overbaugh
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Corresponding author
Summary: 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. Methods to define the antibody-antigen interactions that determine specificity or allow escape have not kept pace. We developed Phage-DMS, a method that 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 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 interactions.
