Human and murine clonal CD8+ T cell expansions arise during tuberculosis because of TCR selection

The immune system can recognize virtually any antigen, yet T cell responses against several pathogens, including Mycobacterium tuberculosis, are restricted to a limited number of immunodominant epitopes. The host factors that affect immunodominance are incompletely understood. Whether immunodominant epitopes elicit protective CD8+ T cell responses or instead act as decoys to subvert immunity and allow pathogens to establish chronic infection is unknown. Here we show that anatomically distinct human granulomas contain clonally expanded CD8+ T cells with overlapping T cell receptor (TCR) repertoires. Similarly, the murine CD8+ T cell response against M. tuberculosis is dominated by TB10.44-11-specific T cells with extreme TCRß bias. Using a retro genic model of TB10.44-11-specific CD8+ Tcells, we show that TCR dominance can arise because of competition between clonotypes driven by differences in affinity. Finally, we demonstrate that TB10.4-specific CD8+ T cells mediate protection against tuberculosis, which requires interferon-? production and TAP1-dependent antigen presentation in vivo. Our study of how immunodominance, biased TCR repertoires, and protection are inter-related, provides a new way to measure the quality of T cell immunity, which if applied to vaccine evaluation, could enhance our understanding of how to elicit protective T cell immunity.This work was supported by the Portuguese Foundation for Science and Technology individual fellowship (CNA) www.fct.pt, a National Institutes of Health Grant R01 AI106725 (SMB) www.nih.gov, and a Center for AIDS Research Grant P30 AI 060354 (SMB) www.nih.gov. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Stabilizing the Peace After Civil War: An Investigation of Some Key Variables

Bosnia, East Timor, Kosovo, Sudan: these and other civil wars haveposed seemingly intractable challenges to policymakers, scholars, andhuman rights groups seeking to put an end to such deadly conflicts. Inthe wake of negotiated settlements to civil wars, one of the thorniestproblems involves reassuring people who have been killing one anotherwith considerable enthusiasm and success that conflict is not about tobreak out again, endangering people s lives. Those concerned with theimplementation and ultimate success of negotiated settlements havedebated how best to enhance the prospects of a stable peace. Whatarrangements, if any, can be used to persuade communities thatintergroup relations will take place in a climate of relative security?Are there any mechanisms the international community might employ todiscourage the resumption of violence? Is an enduring peace settlementmore likely in certain environments than in others? In this researchnote we explore variables that help to explain the longevity ofnegotiated peace settlements.

DFT data associated with Set of Small Ordered Structures (SSOS) paper by Kuner, Rothchild, Asta, and Chrzan (2024). https://doi.org/10.1016/j.commatsci.2024.112924

This repository contains a summary of all DFT data used in the paper (https://doi.org/10.1016/j.commatsci.2024.112924), including input parameters, significant outputs, etc.</p

Retrogenic T cell priming and acquisition of effector functions.

<p>(<b>a</b>) Kinetic analysis of frequency (filled circles) and number (opened circles) of activated (CD44^HiCD62L^Lo) Rg cells in the draining LN (left panel) and lung (right panel) following adoptive transfer into mice infected with <i>M</i>. <i>tuberculosis</i>. (<b>b</b>) Kinetic analysis of frequency of divided Rg cells in the draining LN, lung and spleen following adoptive transfer into mice infected with <i>M</i>. <i>tuberculosis</i>. (<b>c</b>) Kinetic analysis of frequency of IFNγ-producing Rg cells in the draining LN (left panel) and lung (right panel) following adoptive transfer into mice infected with <i>M</i>. <i>tuberculosis</i>. Data are representative from two (b) or three (a, c) independent experiments, each with 5 mice per group. (<b>a,c</b>) One way ANOVA with Dunnett’s post test to compare differences over time (vs. day 7 [<b>a</b>] or d11 [<b>c</b>]) time points. P<0.05 indicated by asterisks (phenotype or IFNγ) or hash marks (cell numbers). (<b>b</b>) One way ANOVA with Tukey’s post test to compare differences in proliferation between lung, LN and spleen; p<0.05 indicated by asterisks.</p

Precursor frequency of TB10.4-specific T cells.

<p>(<b>a,b</b>) Frequency of TB10.4_4-11-specific CD8⁺ T cells in naïve C57BL/6J mice. (<b>a</b>) Represented are dot plots of dual tetramer staining in CD8⁺ T cells in the unbound (left) or bound (right) fractions after immunomagnetic enrichment using tetramers. (<b>b</b>) Quantification of TB10.4_4-11-specific CD8⁺ T cells in naïve C57BL/6J mice, either as the total number (left panel) or as the frequency among CD8⁺ T cells (right panel). Data are representative from two experiments with 6–10 mice. (<b>c,d,e</b>) Frequency of TB10.4_4-11-associated TCRβ DNA (<b>c</b>) or amino acid (<b>d,e</b>) sequences in the T cell repertoire of uninfected C57BL/6J mice. (<b>c</b>) The unique TB10.4_4-11-associated TCRβ DNA sequences from lung#2 were compared pairwise to the TCRβ repertoire of three uninfected mice (spleen A-C). The frequency of unique TCRβ DNA sequences from uninfected mice are on the y-axes (blue); from <i>M</i>. <i>tuberculosis</i> infected lung on the x-axes (red); and sequences detected in both samples are colored purple. The number of unique sequences in each class is indicated in parentheses. (<b>d</b>) A pairwise comparison of unique TB10.4_4-11-associated CDR3β amino acid sequences from lung#2 and uninfected spleen B. (<b>e</b>) The frequency distribution of unique CDR3β amino acid sequences in the uninfected TCR repertoire. ‘Uninfected’ consists of all sequences from uninfected C57BL/6 mice. ‘TB10-specific’ are the TB10-specific sequences found in the uninfected splenic repertoire; ‘shared sequences’ are TB10-specific sequences detected in more than 2 infected mice; ‘expanded sequences’ are all “shared sequences” with frequency >1% in at least one infected mouse. Box represents minimum and maximum, and bar and dot is the median frequency. NS, not significant; ****, p < 0.0001, by one-way ANOVA with Kruskal-Wallis post test.</p

Clonal expansions of CD8+ T cells specific for the immunodominant antigen TB10.4.

<p>(<b>a</b>) Clonality of CD8+ TCR sequences obtained from infected lung granulomas (n = 6) compared to splenocytes from uninfected mice (n = 9); p = 0.0004 by Mann-Whitney. (<b>b,c</b>) Frequency of TCR Vβ families (<b>b</b>) and CDR3βs (<b>c</b>) of TB10.4_4-11-specific CD8⁺ T cells from the lungs of C57BL/6J mice infected with <i>M</i>. <i>tuberculosis</i> for 9 weeks. Data were obtained by Next-generation sequencing of tetramer-purified T cells from 6 individual mice. (<b>d</b>) Frequency of TCR Vβ4 (TRBV2), Vβ5 (TRBV12), Vβ7 (TRBV29), Vβ10 (TRBV4) and Vβ11 (TRBV16) families of TB10.4_4-11-tetramer⁺CD8⁺T (red) or TB10.4_4-11-tetramer^-CD8⁺T (blue) cells from the pulmonary LN of C57BL/6J mice infected with <i>M</i>. <i>tuberculosis</i> at 21 days post infection. (<b>e</b>) Frequency of TCR Vβ4 (TRBV2), Vβ7 (TRBV29) and Vβ10 (TRBV4) families of CD8⁺ T cells from the pulmonary LN or lung of C57BL/6J mice infected with <i>M</i>. <i>tuberculosis</i> at 21 days (left panel), 28 days (middle panel) or >25 weeks (right panel) post infection. Dotted lines connect data from individual mice, some of which are labeled (A through I) to highlight mice with biased Vβ family usage. Data were obtained by flow cytometric analysis of TB10.4_4-11-tetramer⁺CD8⁺ T cells (Tet+) or TB10.4_4-11-tetramer^-CD8⁺ T cells (Tet-) from three independent experiments, each with 4–10 mice per group.</p