In the vast majority of vaccine trials, the primary readouts are empirical do not collect information about the immunological determinants of a vaccine's success or failure. In recent years, several vaccine studies have combined high-throughput transcriptomic data with measures of antigenicity. These systems vaccinology studies have proven invaluable insight into the determinants of efficacy and antigenicity, and have demonstrated the enormous value in mechanistic studies of human vaccination. However, one area that is particularly understudied is the composition of antigen specific receptors that arise during successful and unsuccessful vaccinations. Collection of antigen-specific clonotype information in clinical vaccine studies would provide valuable data that could be used to accelerate vaccine development. The utility of current methodology for repertoire sequencing for immunological studies has been limited due to several factors (i) high-cost and low-throughput of cloning based assays (ii) most high-throughput assays only provide information on a single gene(typically the H-chain of immunoglobulin or -chain for TCRs), or (iii) do not link ag-receptor sequences with immunophenotypic or transcriptomic data. In preliminary work, we have developed a protocol that simultaneously queries the transcriptome and paired antigen receptor sequences in B lymphocytes derived from human bone marrow after flu vaccination using next generation sequencing. The goal of this proposal is to complete development of this combined -Seq assay for both B and T cells, including establishment of its limitations and benchmark against contemporary repertoire sequencing techniques.
Current vaccine trials use efficacy to enhance the immune response against infection as their primary readout, but do not collect data that would help to understand the biological reasons that determine success or failure. Moreover, most vaccines act by stimulating the adaptive arms of the immune system, B and T cells, to make protective antibodies or antiviral responses, however data on the sequence of the protective molecules is almost never collected. Human vaccination offers a unique opportunity to study the immune system in a safe, clinically relevant manner. The goal of this project to develop methods that would greatly expand the immunological data that can be collected from human vaccine trials using recent advances in next generation sequencing.
| Upadhyay, Amit A; Kauffman, Robert C; Wolabaugh, Amber N et al. (2018) BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data. Genome Med 10:20 |
| Havenar-Daughton, Colin; Sarkar, Anita; Kulp, Daniel W et al. (2018) The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen. Sci Transl Med 10: |
