Fig. 4: Mtb-specific T cells exhibit distinct activation phenotypes in RSTR compared to LTBI.

a, GO terms related to T cell activation in clonally expanded ESAT6/CFP10-specific CD4⁺ T cells among RSTR (cell number, 231) compared to LTBI (cell number, 293) from the discovery household contact based on SELECT-seq. b, Expressions of activation and costimulation genes in RSTR and LTBI, as in a. Statistical significance was calculated by two-sided Wilcoxon rank-sum tests with the Bonferroni method. **Adjusted P value <0.005, ***adjusted P value <0.001. c, Interaction network of DEGs related to T cell activation upregulated in RSTR compared to LTBI, as in a. d, Mean expression of T_reg cell-associated genes within each RSTR and LTBI, as in a. e, A box plot showing the median and interquartile range of frequencies of FOXP3⁺CD25⁺ T_reg cells in ESAT6^/CFP10-specific CD4⁺ T cells from the same RSTR (n = 3) and LTBI (n = 4) participants as in a using index sorting and targeted transcriptomics. The whiskers represent minima and maxima. No statistical test was performed due to small sample sizes. f, Gating strategy for CD25⁺ T cells and Foxp3⁺CD25⁺ T_reg cells in ESAT6/CFP10-specific CD4⁺ T cells from RSTR (n = 17) and LTBI participants (n = 20) in the validation household contact cohort. g, Frequencies of CD25⁺CD4⁺ T cells in ESAT6/CFP10-specific CD4⁺ T cells are shown as in f. h, Frequencies of Foxp3⁺CD25⁺ T_reg and IL-10⁺ CD4⁺ T cells in ESAT6^/CFP10-specific CD4⁺ T cells are shown as in f. i, MFIs of IL-10 in supernatants after 48 h ESAT6/CFP10 or 12 h Mtb lysate stimulation based on multiplex cytokine analysis. Significance was determined by two-sided Student’s t-test. Significance in g and h was determined by two-sided Wilcoxon rank-sum tests.