Comprehensive Approaches to Identifying the Targets of Natural and Synthetic Antibodies Using Microarray DNA Synthesis and High-Throughput Sequencing

Abstract

The incredible flexibility and specificity of the humoral immune response is dependent on the highly diverse repertoire of naïve and affinity-matured antibodies. Utilizing and understanding the power of this response requires high-throughput approaches. This thesis describes three projects that use recent advances in DNA sequencing and synthesis to develop and apply methods to probe the diversity of these responses at unprecedented depth. Chapter 2 describes a synthetic antibody library designed for high-throughput sequencing assisted selection which enables rapid in vitro selection of antibodies that bind specifically to a target of interest by bypassing the need for laborious single-clone screening for specific binding. Chapter 3 describes a high-throughput assay for detection of antibodies against all known human viruses using immunoprecipitation and high-throughput sequencing of bacteriophage displaying a library of peptides tiling through the proteome of all known human viruses. And last, chapter 4 describes the use of immunoprecipitation and high-throughput sequencing of both bacteriophage displayed peptides from the human peptidome and ribosome displayed proteins from the human proteome to identify a novel subclass of patients with scleroderma with autoantibodies against the minor spliceosome complex. The work described in this thesis will enhance our ability to study and exploit the properties of antibodies and the humoral immune response.