New Tools for T Cell Identification and Analysis

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Most clinically relevant blood samples are characterized by a limited number of cells available for analysis combined with a low frequency of the T cell populations of interest. Current methodologies for analysis of these samples often require extensive in vitro manipulation and/or assumptions about the antigen specificity and function of the cell populations of interest. The overall goal of this project is to develop new technology that will improve ex vivo analysis of T cell specificity and function, by taking advantage of advances in bioinformatics, proteomics, protein engineering, and array technology. There are five specific aims. Aim 1 is to improve epitope discovery practice, by developing bioinformatics-based epitope prediction algorithms, by applying recent advances in mass spectrometry to identify naturally processed MHC-bound peptides, and by measuring MHC-peptide kinetic lifetimes rather than equilibrium binding affinities. Aim 2 is to develop novel MHC oligomers to extend tetramer staining technology to characterization of heterologous immune responses and characterization of moderate-affinity and low-avidity T cells. Aim 3 is to develop MHCpeptide arrays and ARC arrays, The arrays will be used for functional characterization of T cells after antigen-specific capture and/or activation. Aim 4 is to optimize ex vivo expansion of T celts using nonspecific expansion and antigen-specific stimulation protocols, and to develop new methods for antigenspecific enrichment, expansion, immortalization of T cell populations. Aim 5 is to develop methodology for high-throughput T cell cloning and analysis, including development of microscale culture methods and application of high-throughput screening methodology to T cell characterization. Once developed and validated, these technologies will be applied to T cell identification and analysis experiments in the associated Research Projects.