Mtb-specific CD4 ⁺ T cells express signature effector genes in response to infected macrophages. (A and B) (A) Overlaid line graph and (B) correlation plot of percent T cells per cluster that mapped Mtb-specific (blue) and viral pathogen-specific (red) TCRs. Linear regression (black dashed line) and Pearson’s correlation coefficient squared (r²) are shown. Red and blue dashed circles identify UMAP clusters with highest enrichment of Mtb-specific and viral pathogen-specific TCRs, respectively. (C) Heatmap showing top 10 DEGs normalized to the individual maximum expression for listed clusters. Gene expression patterns common to cluster enriched for Mtb-specific TCRs are outlined. (D) Dot plot showing Reactome pathway overrepresentation analysis using the lists of genes with Log₂FC > 1 for UMAP clusters 4, 6, and 11–15. The list of top seven most significant pathways is arranged based on the GeneRatio (number of input genes associated with a Reactome term/total number of input genes). (E) Summary of receptor–ligand pairs identified by NicheNet analysis, estimating the cell–cell communication (prior interaction potential) between “sender” clusters 4, 11, 13, or 15 (combined) and “receiver” cluster 6 (left), cluster 12 (middle), and cluster 14 (right).