Fig. 2: Mtb-specific T cells exhibit unique phenotypes and are clonally expanded in RSTR.

a, The gating strategy is shown for the sorting of ESAT6/CFP10-specific T cells from RSTR and LTBI in the discovery household contact cohort, based first on the expression of the activation marker CD69 and then CD154 or CD137. b, A heat map showing the median marker expression of ESAT6/CFP10-specific CD4⁺ T cell subsets from three RSTR and four LTBI participants in the discovery household contact cohort. Clustering was performed on flow cytometry mean fluorescence intensities and binarized read counts of profiled genes. c, Dimensionality reduction (t-SNE) projection of ESAT6/CFP10-specific CD4⁺ T cell subsets, as in b. The arrows highlight cluster 6 and cluster 11, which were preferentially detected in RSTR or LTBI participants, respectively. d, Distribution of clonal expansion based on TCRβ chain from single-cell targeted transcriptomics in ESAT6/CFP10-specific T cells, as in b. Each dot represents a clone as defined by the TCRβ chain CDR3 sequence. The size of the dot is proportional to the frequency, which is also depicted as log₂(counts) on the y axis. e, A box plot showing the median and interquartile range of frequency of TCRβ clonal expansion in ESAT6/CFP10-specific CD4⁺ T cells with whiskers representing minima and maxima. No statistical test was performed due to the small sample sizes. f, A histogram indicating the proportion of clonally expanded cells in ESAT6/CFP10-specific CD4⁺ T cell clusters (clusters 1–19), as in b, which were detected more than once in participants among the household contact cohort.