Allergen T cell epitopes during the management of peanut allergic disease

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Project Summary The Gene expression and Systems Immunology (GeSI) Core will provide support for this center by implementation of advanced analysis of flow and mass cytometry (CyTOF), and bulk and single cell RNA- sequencing (RNA-seq). Work in the Core to achieve this function will be organized around three technologies. We will utilize advanced analysis techniques of multi-color flow cytometry and mass cytometry data to elucidate selected phenotypic properties of peanut allergen-reactive CD4+ T cells. These studies will complement standard flow and mass cytometry analyses performed in the PI's laboratories in project-specific experiments. We will use RNA-seq to elucidate full transcriptome phenotypes of bulk populations of peanut allergen specific CD4+ T cells. Knowledge from these experiments will drive design of better flow and mass cytometry experiments in the individual projects, and will aid in analysis of single cell RNA- sequencing (RNA-seq) experiments. We will utilize novel technologies to perform single cell analysis of transcriptome phenotypes and TCR clonotypes of allergen-specific CD4+ T cells. These experiments will facilitate understanding of heterogeneity of allergen-specific CD4+ T cells in PA and in determining mechanism(s) involved in successful OIT. Together, we expect the technologies we provide to play a major role in completion of the component projects, and in driving improved understanding of immune aspects of PA. We also anticipate identifying new biomarkers, new targets and better strategies for patient selection in OIT.