Abstract
CD8+ T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8+ T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labeled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8+ T cells under different antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2, and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8+ T cells from unselected populations. Gene response profiles of CD8+ T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors.
Highlights
CD8+ T cells are integral to the clearance of virus-infected cells and the control of cell transformation
We demonstrate marked downregulation of T cell receptors (TCR) upon stimulation with the cognate peptide and describe protein and gene sets that can be used to identify and isolate antigen-responsive CD8+ T cells. We show how these approaches can be combined with major histocompatibility complex (MHC) multimers to obtain a comprehensive description of activated and non-activated antigen-specific CD8+ T cells, and how they can be used without MHC multimers for identification and in-depth gene expression profiling of cells responding to their cognate antigen
Consistent with the impaired detection of antigenresponsive cells via multimers when cells had been exposed to their cognate peptide, the multimer fluorescence intensity of dyelabeled cells incubated with their cognate antigen was lower than that of cells incubated with solvent or mock peptide (Figure 1C, top)
Summary
CD8+ T cells are integral to the clearance of virus-infected cells and the control of cell transformation. These attributes are exploited by therapies, such as vaccination against infection and immune therapies targeting cancer. CD8+ T cells undergo rapid clonal expansion and this expansion of activated CD8+ T cells can be a marker of ongoing infection in immune-mediated disease. It is conceivable that the detection and information provided by clonal expansions can be used to identify target antigens or disease-causing agents, and to develop therapies that exploit CD8+ T cell specificity to control disease.
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