Fig. 1: IFN-γ-independent T cell responses are not detected in low-exposure controls.

a, Representative flow cytometry showing the expression of IFN-γ and CD154 in CD4⁺ T cells from TST⁻IGRA⁻ or LTBI in the low-exposure cohort in response to ESAT6/CFP10 stimulation. b, COMPASS-generated probability heat map of CD4⁺ T cell subsets including IFN-γ⁻IL-2⁺CD154⁺, IFN-γ⁺IL-2⁻CD154⁺, IFN-γ⁺IL-2⁺CD154⁻ and IFN-γ⁺IL-2⁺CD154⁺ cells from TST⁻IGRA⁻ or LTBI in the low-exposure cohort in response to ESAT6/CFP10. The depth of purple shading correlates to the probability of a participant-specific response above background for a given cell subset. White, no function; black/gray, presence of a function. IFN-γ⁺ cell subsets are noted in gray. c, The frequencies of COMPASS-identified CD4⁺ T cell subsets are shown, background corrected by subtracting the frequency of each subset after DMSO stimulation from the frequency after ESAT6/CFP10 stimulation as in b. d, The frequencies of polyfunctional CD4⁺ T cells that expressed two or more cytokines in response to ESAT6/CFP10 in CD4⁺ T cells as in c. e, Polyfunctionality score of CD4⁺ T cells specific to ESAT6/CFP10. In c−e, the statistical significance was calculated using the Wilcoxon rank-sum test. Two-sided P values are shown, while in c the reported P values were adjusted for multiple hypothesis testing using the Bonferroni method.