Abstract
T cell receptor (TCR) clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cell’s transcriptional program with its TCR identity allow monitoring of T cell clonotype-specific transcriptional dynamics. While these technologies have been available for human and mouse T cells studies, they have not been developed for Rhesus Macaques (RM), a critical translational organism for autoimmune diseases, vaccine development and transplantation. We describe a new pipeline, ‘RM-scTCR-Seq’, which, for the first time, enables RM specific single cell TCR amplification, reconstruction and pairing of RM TCR’s with their transcriptional profiles. We apply this method to a RM model of GVHD, and identify and track in vitro detected alloreactive clonotypes in GVHD target organs and explore their GVHD driven cytotoxic T cell signature. This novel, state-of-the-art platform fundamentally advances the utility of RM to study protective and pathogenic T cell responses.
Highlights
Expression of the highly polymorphic [1] T cell receptor (TCR) allows T cells to recognize foreign and self-antigens presented in the context of the Major Histocompatibility Complex (MHC) by antigen presenting cells
TCR repertoire analysis has become a fundamental tool to understand the immune responses to infections and vaccines, as well as the immunopathogenesis of rejection after solid organ transplantation, and graftversus-host disease (GVHD) after hematopoietic stem cell transplant (HCT) [2, 46, 47, 54,55,56,57,58]
In murine and human studies, the introduction of VDJ target enrichment combined with single cell sequencing platforms has enabled the interrogation of transcriptional profiling of single T cells at an unprecedented level of accuracy [42, 43]
Summary
Expression of the highly polymorphic (up to 1018 specificities) [1] T cell receptor (TCR) allows T cells to recognize foreign and self-antigens presented in the context of the Major Histocompatibility Complex (MHC) by antigen presenting cells This diversity is achieved by complex genetic recombination of the T cell alpha and beta chain during thymic T cell development, and results in a unique molecular barcode for each T cell. The study of human single cell TCR data continues to focus predominantly on the peripheral blood, being restricted by inherent challenges in accessing human tissues during health and disease This can result in an incomplete picture of important immunological processes when using human samples
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