Simultaneous antigen receptor repertoire profiling and single-cell transcriptomics in T and B lymphocytes from limited clinical samples

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 DESCRIPTION (provided by applicant): 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 ß-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.