Simultaneous antigen receptor repertoire profiling and single-cell transcriptomics in T and B lymphocytes from limited clinical samples
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Principal Investigator: Steven Edward Bosinger Organization: EMORY UNIVERSITY Fiscal Year: 2019 Award: $379,584 Funding agency: National Institute of Allergy and Infectious Diseases 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. Terms: <ATGN><Alleles><Allelomorphs><Anti-Viral Response><Antibody Response><Antigen Receptors><Antigens><Antiviral Response><Area><Assay><B blood cells><B cell><B cells><B-Cells><B-Lymphocytes><B-cell><Benchmarking><Best Practice Analysis><Binding><Bioassay><Biologic Assays><Biological><Biological Assay><Biopsy Sample><Biopsy Specimen><Blood><Blood Coagulation Factor I><Blood Coagulation Factor One><Blood Factor One><Blood Reticuloendothelial System><Bone Marrow><Bone Marrow Reticuloendothelial System><CD8 Cell><CD8 T cells><CD8 lymphocyte><CD8+ T cell><CD8+ T-Lymphocyte><CD8-Positive Lymphocytes><CD8-Positive T-Lymphocytes><Cell Body><Cells><Cellular Assay><Clinical><Clinical Trials><Cloning><Coagulation Factor I><Coagulation Factor One><Collection><Computational algorithm><Data><Development><Differential Gene Expression><Factor I><Factor One><Failure><Fibrinogen><Flu vaccination><Genes><Genomics><Goals><High Throughput Assay><Human><Immune Globulins><Immune response><Immune system><Immunochemical Immunologic><Immunoglobulins><Immunologic><Immunological><Immunological response><Immunologically><Immunologics><Individual><Infection><Influenza immunization><Influenza vaccination><Light><Measures><Messenger RNA><Methodology><Methods><Modern Man><Molecular Interaction><Monitor><Mucosa><Mucosal Tissue><Mucous Membrane><NGS Method><NGS system><Non-Polyadenylated RNA><Photoradiation><Population><Procedures><Prophylactic vaccination against influenza><Protocol><Protocols documentation><RNA><RNA Gene Products><RNA Seq><RNA sequencing><RNAseq><Receptor Protein><Retrieval><Ribonucleic Acid><Sampling><System><T cell response><T-Cells><T-Lymphocyte><T8 Cells><T8 Lymphocytes><Technical Expertise><Techniques><Testing><Tissue-Specific Differential Gene Expression><Tissue-Specific Gene Expression><Translating><Vaccination><Vaccines><Validation><Work><allergic/immunologic body system><allergic/immunologic organ system><antigen-specific T cells><arm><base><cell assay><clinical relevance><clinically relevant><computer algorithm><cost><cost effectiveness><develop a vaccine><development of a vaccine><developmental><flu immunisation><global gene expression><global transcription profile><high throughput screening><high throughput technology><host response><immunogen><immunoresponse><improved><influenza virus vaccination><insight><mRNA><mRNA sequencing><mRNA-seq><next gen sequencing><next generation sequencing><nextgen sequencing><prospective><public health relevance><receptor><rectal><success><technical skills><thymus derived lymphocyte><transcriptome><transcriptome sequencing><transcriptomics><vaccination against influenza><vaccination study><vaccination trial><vaccine development><vaccine formulation><vaccine study><vaccine trial><vaccinology>