High-Throughput Approaches to Profiling Antibody and T Cell Targets

Abstract

B and T lymphocytes are potent effector cells of the adaptive immune system that recognize antigens through antibodies and T cell receptors (TCRs) respectively. Together, they orchestrate antigen-specific responses and generate long-term immune memory. The recognition of specific antigens by B and T cells mediates protection from pathogens and controls neoplasias, but can also cause autoimmunity. However, our knowledge of immune function in each of these contexts is limited by the difficulty of systematically profiling the targets of antibodies and TCRs. Motivated by this challenge, this dissertation presents two tools to map the targets of antibodies and CD8 T cells in high throughput. The first part of this dissertation describes VirScan, a high-throughput method to comprehensively analyze antiviral antibodies. VirScan uses immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide peptides from all human viruses. We assayed over 108 antibody-peptide interactions in 569 humans across four continents, nearly doubling the number of previously established viral epitopes. We detected antibodies to an average of 10 viral species per person and a set of 84 species in at least two individuals. Although rates of specific virus exposure were heterogeneous across populations, antibody responses targeted strikingly conserved “public epitopes” for each virus, suggesting that they may elicit highly similar antibodies. VirScan is a powerful approach for studying interactions between the virome and the immune system. The second part of this dissertation describes T-Scan, a high-throughput platform for identification of antigens productively recognized by T cells. T-Scan uses lentiviral delivery of antigen libraries into cells for endogenous processing and presentation on MHC molecules. Target cells functionally recognized by T cells are isolated using a reporter for granzyme B activity and the antigens mediating recognition are identified by nextgen sequencing. We show that T-Scan correctly identifies cognate antigens of TCRs from viral and human genome-wide libraries. We apply T-Scan to discover new viral antigens, perform high-resolution mapping of TCR specificity, and characterize the reactivity of a tumor-derived TCR. T-Scan is a powerful approach for studying T cell responses.