Fig. 4: Transcriptional profiles and clonal diversity of EBV-specific T cells in young adults depend on antigen-specificity.

A Schematic of single-cell RNA-seq studies of antigen-specific CD8⁺ T cells from 7 young (Y, < 40 years, mean age of 31.9 years) and 7 older (O, > 65 years, mean age of 71.1 years) adults. BEAM-T (Barcode Enabled Antigen Mapping of T cells) was employed. Antigen-specific T cells were live, single cells that were CD8⁺ and stained positive for the BEAM-T conjugate (which included a PE fluorophore, see the Methods for additional information). Total CD8⁺ T cell subpopulations that were negative for the BEAM-T conjugate were included as well. B Bubble plot of antigen-specific T cell proportions among clusters defined in Supplementary Fig. 6A. The bubble size and color reflect the proportion of antigen-specific T cells in a given cluster. C Probability vectors describing the subset distribution of antigen-specific T cells were compared. Significance levels between the indicated pairwise comparisons are shown as bubble size and color. D PCA based on cell subset frequencies. E K-means clustering of differentially expressed genes in any binary pseudobulk comparison of antigen-specific memory T cell populations. Pathway and annotation enrichment in each K-means cluster and selected genes are shown on the right. F T cell receptor (TCR) diversity and clonality are shown as the Inverse Simpson index and Gini index, respectively. 7 Y and 7 O adults were assessed, but only cells with TCRα and TCRβ sequences in single-cell sequencing data and samples with ≥20 cells were used for the calculation. G Cumulative TCR clone numbers depicting the numbers of distinct antigen-reactive TCR chains ordered by decreasing clonal sizes plotted against the cumulative space they occupy. Line graphs with different colors illustrate the clonal size distributions for different antigen specificities. All datapoints represent distinct biological replicates. Data show the median (B) or mean ± SEM (F). Data were compared by two-sided permutation tests (D). Source data are provided as a Source Data file.