MR1-restricted T cell clonotypes are associated with “resistance” to Mycobacterium tuberculosis infection
Deborah L. Cross, Erik D. Layton, Krystle K.Q. Yu, Malisa T. Smith, Melissa S. Aguilar, Shamin Li, Elise C. Wilcox, Aude G. Chapuis, Harriet Mayanja-Kizza, Catherine M. Stein, W. Henry Boom, Thomas R. Hawn, Philip Bradley, Evan W. Newell, Chetan Seshadri
Deborah L. Cross, Erik D. Layton, Krystle K.Q. Yu, Malisa T. Smith, Melissa S. Aguilar, Shamin Li, Elise C. Wilcox, Aude G. Chapuis, Harriet Mayanja-Kizza, Catherine M. Stein, W. Henry Boom, Thomas R. Hawn, Philip Bradley, Evan W. Newell, Chetan Seshadri
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Research Article Immunology Infectious disease

MR1-restricted T cell clonotypes are associated with “resistance” to Mycobacterium tuberculosis infection

Abstract

T cells are required for protective immunity against Mycobacterium tuberculosis. We recently described a cohort of Ugandan household contacts of tuberculosis cases who appear to “resist” M. tuberculosis infection (resisters; RSTRs) and showed that these individuals harbor IFN-γ–independent T cell responses to M. tuberculosis–specific peptide antigens. However, T cells also recognize nonprotein antigens via antigen-presenting systems that are independent of genetic background, known as donor-unrestricted T cells (DURTs). We used tetramer staining and flow cytometry to characterize the association between DURTs and “resistance” to M. tuberculosis infection. Peripheral blood frequencies of most DURT subsets were comparable between RSTRs and latently infected controls (LTBIs). However, we observed a 1.65-fold increase in frequency of MR1-restricted T (MR1T) cells among RSTRs in comparison with LTBIs. Single-cell RNA sequencing of 18,251 MR1T cells sorted from 8 donors revealed 5,150 clonotypes that expressed a common transcriptional program, the majority of which were private. Sequencing of the T cell receptor α/T cell receptor δ (TCRα/δ) repertoire revealed several DURT clonotypes were expanded among RSTRs, including 2 MR1T clonotypes that recognized mycobacteria-infected cells in a TCR-dependent manner. Overall, our data reveal unexpected donor-specific diversity in the TCR repertoire of human MR1T cells as well as associations between mycobacteria-reactive MR1T clonotypes and resistance to M. tuberculosis infection.

Authors

Deborah L. Cross, Erik D. Layton, Krystle K.Q. Yu, Malisa T. Smith, Melissa S. Aguilar, Shamin Li, Elise C. Wilcox, Aude G. Chapuis, Harriet Mayanja-Kizza, Catherine M. Stein, W. Henry Boom, Thomas R. Hawn, Philip Bradley, Evan W. Newell, Chetan Seshadri

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Figure 5

Immunosequencing reveals MR1T and DURT clonotypes that are significantly enriched among RSTRs.

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Immunosequencing reveals MR1T and DURT clonotypes that are significantly...
(A) PBMCs from RSTR (n = 19) and LTBI (n = 20) were analyzed using TCRα/δ immunoSEQ (Adaptive Biotechnologies). Simpson’s clonality was calculated for each donor’s repertoire and stratified by group. (B) Bar plot showing the number of TCRα/δ clonotypes that were shared between donors (n = 39) (C) Volcano plot of TCRα/δ clonotypes after testing for enrichment in RSTR or LTBI groups. Enriched clones are highlighted in red. MR1T clonotypes identified previously in scTCR-Seq are highlighted in yellow. A clonotype was defined by CDR3α amino acid sequence and V- and J-gene identity. Enriched clones were identified by 2-sided Fisher’s exact test using a P value threshold of 0.01 (adjusted for multiple testing) (threshold indicated by dashed line on the plot). (D) Box plot of frequencies of MR1T clonotypes previously defined in scTCR-Seq analysis that were also identified among enriched clones in the volcano plot. Matching was based on CDR3α amino acid sequence and V- and J-gene identity. Displayed P values were calculated using Fisher’s exact tests and are unadjusted for multiple testing. (E) Box plot of frequency of canonical MAIT TCRα stratified by group. Displayed P value was calculated using Wilcoxon rank sum test. (F) Heatmap of frequencies (as a proportion of templates per sample) of TCRα/δ clonotypes found exclusively among either RSTR or LTBI donors and P < 0.05 by Fisher’s exact test. Unadjusted P values were used to select clonotypes for inclusion in the heatmap. A P value of less than 0.05 was considered significant. For all box plots, the upper whisker extends to the highest value within 1.5× IQR, and the lower whisker extends to the lowest value within 1.5× IQR. The horizontal line in the center of the box reflects the median value of the data.