Core 3: Single-Cell Core

Project Summary – Single-Cell Core Recent advances in single-cell technologies have revolutionized the field of antibody discovery. The Single-Cell Core part of this proposal will utilize a variety of cutting-edge technologies to facilitate and support the efforts of the two Projects. A critical advantage of our efforts for identifying C. difficile-specific antibodies is our recently developed LIBRA-seq technology (LInking B-cell Receptor to Antigen specificity through sequencing). LIBRA-seq is an innovative platform for antibody discovery and characterization of antigen- specific antibody repertoires. Unlike other approaches for antibody discovery, LIBRA-seq is the first to enable the simultaneous determination of B cell receptor sequence and antigen specificity for a large number of B cells against a theoretically unlimited number of diverse antigens, at the single-cell level. LIBRA-seq therefore provides a unique opportunity to include multiple different antigens as part of the screening library for targeted and efficient discovery of antigen-specific antibodies against different targets on C. difficile. In parallel to our LIBRA-seq efforts that will be focused on utilizing individual C. difficile antigens, we will also work toward the identification of C. difficile-specific B cells by using whole fluorescent bacteria for fluorescent-activated cell sorting, followed by next-generation sequencing of paired heavy-light chains of the B cell receptors of the bacterium-reactive sorted B cells. We will refer to this approach as BUG-seq. With BUG- seq, we will be able to interrogate a broader repertoire of C. difficile-specific B cells that extends beyond the specific antigens that will be utilized for the LIBRA-seq experiments. Indeed, the LIBRA-seq efforts will provide a focused approach to identify C. difficile-specific B cells, while the BUG-seq efforts will cast a wide net for capturing diverse antigen-specific antibodies. The utilization of both LIBRA-seq and BUG-seq will provide highly significant cutting-edge capabilities as complementary approaches for the identification of C. difficile-specific antibodies. Overall, the work proposed here will utilize a variety of techniques, bringing together microfluidics, next-generation sequencing, protein science, and immunology, combined with computational data analysis. Together, these efforts will lead to unparalleled capabilities for understanding antibody responses to C. difficile infection, and for identification of antibody therapeutic candidates against a wide range of epitopes and antigens. The work in the Single-Cell Core is therefore highly significant for the proposed efforts for discovery and characterization of C. difficile-specific antibodies, a fundamental goal for both Projects in this proposal.