The disease which we now know as Tuberculosis (TB) has had many names over the course of history: phthisis, the white plague, robber of youth, Consumption. Caused by the pathogenic bacterium Mycobacterium tuberculosis (M. tb), people who become infected often experience a period of latency, when disease is asymptomatic, before active infection begins, causing debilitating symptoms and a high incidence of mortality. M. tb may constitute the deadliest pathogen in history, claiming millions of lives and even finding its way into literature and art, including an appearance in Les Miserables. In the United States, the pursuit for control of TB has resulted in a dramatic reduction in the prevalence of infection, however, TB still remains a significant concern in many parts of the world.
Fortunately, however, not everyone who comes into contact with someone with TB will be fated to become infected, yet the mechanisms that allow them to ‘resist’ infection are not understood. In aiming to uncover some of the immune-related aspects of resistance, Dr. Deborah Cross in Dr. Chetan Seshadri’s lab at the University of Washington School of Medicine recently published in the Journal of Clinical Investigation Insight on their characterization of specific T cell populations that are associated with this outcome. T cells are specialized immune cells that can form a ‘memory’ of pathogens they’ve previously encountered so that they can respond more swiftly and accurately upon re-exposure. The basis of this is what allows for skin tests, where TB antigen is injected into the skin and will result in a localized immune response if the person has been infected or previously vaccinated. The research team had previously described a cohort of Ugandans with household exposures who never went on to develop active infection after 9.5 years, whom the authors define as resisters (RSTR). While they observed TB-specific, IFNγ -independent T cell responses, indicating exposure, they wanted to further characterize the T cell responses that might help promote this resistance. However, instead of the typical T cells which recognize protein antigens via major histocompatibility complexes (MHC), the team was primarily interested in ‘donor-unrestricted T cells’ (DURTs) which recognize nonpeptide antigens via other proteins such as CD1 or MHC-related protein 1 (MR1).
To uncover whether these DURTs were associated with resistance to TB following exposure, the researchers utilized their cohort of household contacts in Uganda. They chose a sub cohort of RSTRs and latently infected TB (LTBI) participants to assess DURT cell responses in peripheral blood using tetramer staining and flow cytometry, which allows for specific identification of these T cells. They saw that MR1-restricted T (MR1T) cells were the only population of DURT cells which were altered between the groups, where they were found in higher frequencies in the RSTRs. Dr. Cross pointed out that they “were intrigued to see that circulating frequencies of MR1[-restricted] T cells were elevated in individuals that resist signs of clinical infection…in comparison with donors that developed latent infection.” The researchers wanted to see if there were any specific trends in the T cell receptor (TCR) gene sequences of these cells between response outcomes. Since MR1 has low sequence diversity between individuals and many MR1T cells have semi-invariant TCRs (i.e. lacking the sequence changes made throughout T cell development), there can often be seen a good deal of overlap of ‘clonotypes’, or T cells with shared TCR sequences, between individuals. For this, they sorted out MR1T cells and performed single-cell RNA sequencing (scRNA-seq) with TCR sequencing. They found a variation in expansion of clones, unique clones which were only found once, expanded clones which were found up to 50 times, and hyperexpanded clones which were found more than 50 times. However, proportions of the clone expansion sizes were not different between RSTRs and LTBI.
Because they hypothesized that clonotypes would likely be found as shared between individuals, they assessed whether this was the case in their data. They did find that the shared clones were more frequent among the hyperexpanded clones, however, they found very few shared clones overall, with most only being shared between 2 individuals. This suggested to them that there was a higher degree of clonal diversity and unique clones between individuals of these MR1T cells than previously appreciated. Dr. Cross noted that “MR1T cells are expected to express a semi-invariant TCR so this was surprising to see.” The team did, however, note that there were more shared clones between RSTRs than LTBI, indicating that there might be something unique about these clones that could convey resistance to infection. When they analyzed their scRNA-seq data, despite a high degree of TCR diversity, gene profiles of these clonotypes were not remarkably different, suggesting to them that it was likely the ability of the cell to recognize bacterial ligands (based off their TCR) that was providing protection. One of the final questions the research team wanted to address was whether the MR1-TCRs preferentially found in RSTRs were reactive to mycobacteria-infected cells. They expressed these TCR sequences in vitro in T cells and incubated them with cells that had been infected with the related mycobacteria Bacillus Calmette-Guerin (BCG). They found that both TCRs resulted in T cell recognition of the infected cells, providing evidence that populations of MR1T cells expressing these TCRs may represent protective cells in people who resist TB infection.
Altogether, their study provided unique evidence in the case of MR1T cells being associated with resistance to TB infection. Having higher levels of MR1T cells could result from either genetic or microbiome-related differences between individuals, and so the authors speculate that the higher proportions of MR1T cells in RSTRs may result from these intrinsic differences. Dr. Cross explained that animal studies have provided conflicting evidence for the role of MR1T cells, but that, “none of these studies investigated the association between specific MR1T clonotypes and protection from Mtb disease. This may be an important point of consideration for the field going forward.” The team is excited to see if additional studies may provide insight into the role these cells may have during TB infection, or whether this could extend beyond TB, as MR1T cells are involved in recognition of bacterially infected cells.
This Spotlight work was funded by the American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists, the NIH and the Bill and Melinda Gates Foundation.
Fred Hutch/University of Washington/Seattle Children’s Cancer Center Consortium members Drs. Aude Chapuis, Philip Bradley, Evan Newell and Chetan Seshadri contributed to this work.
Cross DL, Layton ED, Yu KK, Smith MT, Aguilar MS, Li S, Wilcox EC, Chapuis AG, Mayanja-Kizza H, Stein CM, Boom WH, Hawn TR, Bradley P, Newell EW, Seshadri C. MR1-restricted T cell clonotypes are associated with "resistance" to Mycobacterium tuberculosis infection. JCI Insight. 2024 May 8;9(9):e166505. doi: 10.1172/jci.insight.166505. PMID: 38716731; PMCID: PMC11141901.