Single-cell transcriptomics reveals distinct phenotypes of memory CD4 ⁺ T cell responses to infected macrophages. (A) UMAP visualization plot including the Louvain clustering of 157,462 cells after integration and quality control from 7 LTBI participants (12 samples, AIM⁺ memory CD4⁺ T cells in response to infected macrophages ± lysate) and 6 non-LTBI participants (6 samples, AIM⁺ memory CD4⁺ T cells in response to infected macrophages). Top DEGs for each cluster are listed below plot, grouped by IFNγ and TNF expression. (B) Kernel density estimation of selected T helper subset genes projected onto the UMAP plot. Density values were reduced to max/min scale. (C) Heatmap with hierarchical clustering (left) showing top five DEGs for each cluster, conserved across treatment groups. (D) Split UMAP plots for experimental groups showing mapping of all TCRs. Expanded (≥2 copies) and nonexpanded (single) TCR clonotypes are shown in red and blue, respectively. (E and F) Representative stacked bar plots showing (E) percent clonally expanded versus nonexpanded TCRs of total TCRs sequenced from LTBI participant samples, and (F) ratio of expanded and nonexpanded TCRs normalized to each cluster’s total cell number. (G and H) Joint density estimation plot for (G) CCR7 and SELL transcripts and (H) pseudotime trajectory (rooted in cells with the highest expression of CCR7 and SELL), projected onto the UMAP plot. Cell fates (gray circles), transition states (black circles), and proximity to (purple) and remoteness from (yellow) the root are indicated.