Immune cell signatures predict progression from Mtb exposure to active tuberculosis

Tuberculosis remains a major global health problem because many people exposed to Mycobacterium tuberculosis (Mtb) never develop active disease, while a subset progress months or years later. Identifying who is at risk after exposure is critical for prevention and for directing vaccines and treatments, but the immune signals that mark that risk are not fully understood. To tackle this, a team led by Spyros A. Kalams studied blood from 57 HIV-negative close contacts of TB cases in Brazil. The group included 25 people who developed active TB within two years (progressors) and 32 matched controls who stayed disease-free (non-progressors). The researchers performed single-cell transcriptional profiling of more than 500,000 peripheral blood mononuclear cells, stimulating these cells so they could identify which immune cells reacted to Mtb. By comparing responses between progressors and non-progressors, the study aimed to find specific, early immune programs that predict progression to active disease and might guide future vaccines or targeted prevention.

The study used separate stimulations with the MTB300 peptide pool and with irradiated Mtb (gRV) to reveal antigen-reactive states across both adaptive and trained-innate immune lineages. Single-cell transcriptional profiling captured detailed gene expression in CD4⁺ T-cells, NK cells, monocytes and other cell types. Adaptive responses included CD4⁺ T-cells expressing abundant cytokines such as IFNG, TNF, and IL17F. Trained-innate responses were seen among NK cells producing GM-CSF, IFNG, CCL3, and CCL4, and among monocytes expressing GM-CSF, IL12B, and IL36G. Comparing progressors and non-progressors, the team found that progressors showed early hyper-metabolic CD4⁺ T-cell programs and proliferative NK cell signatures, whereas non-progressors preferentially upregulated complement activation and CCL3/4-driven chemokine signaling in monocytes. Importantly, within progressors, gene expression profiles in antigen-reactive CD4⁺ T-cells and monocytes were able to predict the timing of progression to active TB.

These findings show that people recently exposed to Mtb harbor high frequencies and a wide functional diversity of antigen-reactive immune cells in the blood. By linking specific transcriptional programs in CD4⁺ T-cells, NK cells, and monocytes to later disease outcomes, the study nominates measurable immune correlates that could be used to identify individuals at higher risk of developing active TB. That information is potentially useful for the rational design of next-generation TB vaccines and for targeting preventive interventions to those most likely to benefit. The results also illustrate how single-cell transcriptional profiling, combined with defined stimuli like the MTB300 peptide pool and irradiated Mtb (gRV), can reveal subtle but meaningful differences in early immune responses after exposure that are otherwise invisible in bulk measurements.