Tuberculosis (TB) is the leading infectious disease killer worldwide, and novel vaccines are desperately needed. Vaccine development is however hampered currently due to a lack of understanding of the immune response to Mycobacterium tuberculosis (Mtb), the causative organism of TB. Aerosol exposure to Mtb results in a wide range of possible outcomes from clearance to development of active disease. Lung-resident immune effector cells are critical in this spectrum and remain poorly understood. MR1-restricted T (MR1T) cells are an innate-like T cell that are enriched in mucosal surfaces, particularly the airway. They are defined by their recognition of bacterial and fungal metabolites, including Mtb, presented from the monomorphic MHC class 1-related molecule (MR1). MR1T cells in the airway could play a specialized role in defense against Mtb, especially early in disease, and may be very valuable either directly in future TB vaccine development or in adjuvant development.
To further explore this, active TB participants were enrolled and their asymptomatic household contacts (HHC). HHC were stratified by PET/CT scan for subclinical disease and blood and bronchoscopy samples were obtained from all participants, as well as active TB participants at the end of treatment. All samples were sorted for MR1T cells, and the single-cell gene-expression and TCR-sequencing was done.
We found that MR1T cells from the blood and lung had very different gene expression profiles, and clustered differently on dimensionality reduction. Using a gene expression score for inflammation we found that this was lowest in lung-derived MR1T cells from control and PET/CT negative individuals, increased in subclinical disease and further increased in active TB before dropping again at the end of treatment. Examining the TCR repertoire, there were significant differences in lung compared to blood TCRs with approximately 20% being tissue-specific. Comparing TCR profiles before and after treatment, we found limited changes, suggesting that removal of ongoing antigen exposure over the 6-month treatment course did not lead to changes in the TCR repertoire of donors. TCR sequences were very private, and to look for TCR enrichments across donors, TCRs were clustered using TCRdist, a method for identifying closely related clonotypes that are likely to respond to the same or similar antigens. There were 9 TCR clusters that were enriched in subclinical or active TB donors compared to those without evidence of active or subclinical disease. These enriched TCR clusters also significantly upregulated cytotoxic and effector genes, and downregulated naïve markers.
Overall, this work suggests that MR1T cells in the lung are directly responding to Mtb in human donors and that there may be specific TCR clusters that are enriched during disease to help combat infection.