﻿Most TCR clonotypes were present in 1C4 samples, which corresponds to the number of samples per individual, although we detected 1 TCR clonotype in 16 samples (Figure 8E)

﻿Most TCR clonotypes were present in 1C4 samples, which corresponds to the number of samples per individual, although we detected 1 TCR clonotype in 16 samples (Figure 8E). was dominated by V1 and distinguished by highly localized clonal expansions, consistent with the nonrecirculating lung-resident T cell population. These data show that repertoire sequencing is a powerful tool for tracking T cell subsets during disease. (Mtb), remains the leading cause of death from an infectious agent (Global Tuberculosis Report, WHO, 2018 (1). Although treatable with antibiotics, there is an urgent need to develop an effective vaccine against TB because of the challenges of diagnosis, the long duration of treatment, and the rise of drug-resistant strains. Protection from disease in 90% of infected individuals demonstrates that immune responses can cope with Mtb infection (2). Bacille Calmette-Gurin (BCG), the current vaccine, protects infants from disseminated TB and may enhance immunity if readministered, or when given by intravenous or aerosol vaccination routes. In addition, BCG can be improved upon, as shown by the recent phase IIb trial of the novel M72/AS01E vaccine (3). These data offer hope that an improved TB vaccine is possible, but more potent Tubastatin A HCl candidates are needed. The potential to harness donor-unrestricted T cells (DURTs) and other unconventional T cells to boost anti-TB immunity is of great interest to the vaccine field (4). Conventional T cells are restricted to recognizing peptide antigens bound to MHC molecules that are highly polymorphic between unrelated individuals. Unconventional T cells, in contrast, generally recognize antigens bound to nonpolymorphic antigen-presenting molecules and are thus unrestricted by the host genotype (5). In addition, they typically target conserved pathogen-derived lipids and metabolites, which are less likely to mutate and be lost as immune targets. DURTs described to date include mucosa-associated invariant T cells (MAITs), FACD HLA-ECrestricted T cells, invariant NK T cells (iNKTs), and group 1 CD1Crestricted T cells including germline-encoded mycolyl lipidCreactive T cells (GEMs). MAITs, iNKTs, and GEMs all recognize their cognate antigens (bacterial metabolites bound to MR-1 or lipid-derived ligands Tubastatin A HCl bound to CD1a, -b, -c, or -d) via T cell receptors (TCRs). In addition, T cells are a major class of unconventional T cells that recognize a variety of peptide and nonpeptide antigens presented by CD1 or other nonpolymorphic molecules via the TCR (6, 7) Many studies indicate that these unconventional T cells play an important protective role in TB, particularly during early infection (8C10). For example, T cells recognize Mtb antigens, respond to BCG vaccination, suppress mycobacterial growth, and confer protection when adoptively transferred, and expansion of pulmonary T cells by vaccination reduces disease pathology in nonhuman primates (NHPs) (11). Likewise, CD1-restricted DURTs recognize mycobacterial lipids, transfer of mycolic acidCspecific CD1b-restricted T cells confers protection against TB to humanized mice, and airway LAM-responsive, CD1b-restricted T cells are associated with protection from Tubastatin A HCl disease in TB-exposed humans (12C14). MR1-KO mice, which lack MAITs, show a reduced ability to control initial infection (15), and polymorphism associated with reduced MR1 expression in humans is linked to TB susceptibility and meningeal disease (16). This anti-TB activity of DURTs and T cells and the universal nature of their presenting molecules make the highly conserved antigens they recognize attractive vaccine targets (9, 16, 17). Another promising feature of DURTs and some subsets is their apparent preference to migrate to and reside at mucosal sites. Promotion of lung residency of TB-specific T cells is thought to be essential for the protective activity of these cells, and this protection may even be highly localized within the particular tissue, as T cell control can vary among different lesions within the same lung (18). This may also explain why it is challenging to identify strong T cell correlates of protection in the blood (19C22). MAITs, for example, are highly enriched at mucosal barriers, including in the lung, where they comprise 2%C4% of T cells (8). Several infections, including TB, are associated with a loss of MAITs from the circulation, which could result from recruitment to infected tissues (8). Likewise, pulmonary CD1Crestricted T cells and T cells isolated from Mtb-infected subjects rapidly migrate back to the lung after intravenous infusion (13, 23). However, little is known about the lung DURT and T cell response in human TB infection, as most studies have focused on blood. The existence of noncirculating tissue-resident memory T cells (Trms) (24) demonstrates that T cell responses in the blood and tissue do not always mirror each other. Therefore, it is necessary to characterize DURT and T cell responses in the lung.