Fig. 6: RSTR CD4⁺ T cell phenotypes associate with lack of progression to active TB in the ACS cohort and bacterial control in NHPs.

a,b, Box plots showing the median and interquartile range of RSTR-associated T_N_T_SCM cell module (a) or T cell activation module scores (b) from whole-blood bulk transcriptomics at serial time points before TB diagnosis among nonprogressors (n = 101) and progressors (n = 43) in the ACS (GSE79362) (ref. ²⁸). The whiskers represent minima and maxima. Scores were computed as geometric mean of gene expressions. Significance was determined by two-sided Student’s t-test. c, Frequencies of Mtb-specific CD4⁺ T cells expressing RORC and/or TBX21 or FOXP3 among TB nonprogressors (n = 35) and progressors (n = 35) in ACS³¹ using single-cell targeted transcriptomics. Significance was determined by two-sided Wilcoxon rank-sum tests. d,e, Heat maps showing the mean expression of the top 15 enriched genes in a stem-like T cell subset (d) and a T1–T17 cell subset (e) identified in granulomas from cynomolgus macaques in clonally expanded ESAT6/CFP10-specific CD4⁺ T cells in RSTR (cell number, 231) and LTBI (cell number, 293) in the household contact cohort. f, Stem-like T cell- and T1–T17 T cell-associated gene module scores as in d. g, RSTR-associated T_H17 cell gene module score from whole-blood bulk transcriptomics in rhesus macaques at day 0 (W0), day 2 (D2), week 2 (W2), week 4 (W4) and week 12 (W12), postintravenous vaccination with BCG. h, Flow cytometry showing cell count and frequency of IFNγ⁻IL-2⁻IL-17⁺TNF⁻ T_H17 CD4⁺ cells in the bronchoalveolar lavage of BCG-vaccinated rhesus macaques as in g. For c and f–h, significance was calculated using the two-sided Wilcoxon rank-sum tests.