Fig. 5: Reorganization of the naive-like memory CD8+ T cell compartment across age.
a, Identification of subsets within CD8+CD27+CD197+CD45RA+ T cells through a trimodal analysis, shown in a 3WNN UMAP plot with the true naive, SCM, MNP-1, MNP-2 and MAIT subsets colored. b, Expression of select RNA and ADT cell type markers, shown in 3WNN UMAP plots. The modality of detection is indicated in square brackets. Density, gene-weighted 2D kernel density. c, Chromatin accessibility tracks of the IFNG gene region in naive CD8+ T cell subsets, showing normalized read coverage. d, Bar plot (median value shown) of the frequencies of naive CD8+ T cell subsets within the overall naive CD8+ compartment by age group (n = 8 per group). P values were determined by a two-tailed Mann–Whitney test with the Holm–Sidak multiple-comparison method. *P < 0.05 (P = 0.02), **P < 0.01 (P = 0.003), ***P < 0.001 (P = 0.0008). e, Age-specific composition of the non-naive compartment found within naive CD8+ T cells. f, 3WNN UMAP plot of all T cells overlaid with naive CD8+ T cell subsets and separated by age. Only cells from the naive CD8+ T cell compartment of children (left) or adults (right) are colored; all other cells are gray. g, Comparison of differential chromatin accessibility across all CD8+ T cell subsets (24,874 features). For visualization, all values are scaled (z score) per differential region. h, Dot plot of select DEGs across naive CD8+ T cell subsets. The size of points corresponds to the fraction of cells expressing each gene; color corresponds to average expression. AvgExp, scaled average expression. i, Identification of the MNP-2 subset through gene expression profiling in the scRNA-seq confirmatory cohort. Density, gene-weighted 2D kernel density. j, MNP-2 subset frequencies within the total T cells across all age groups including an external cord blood (n = 3) dataset.
