Mtb antigens are processed by the cytosolic pathway.

<p>(A,B) Human monocyte-derived DC were treated with epoxomicin, BFA, or bafilomycin for one hour before infection with Mtb H37Rv-eGFP (A) or addition of CFP10 and CFP10_3–11 (B). After 15–16 hours in the presence of the inhibitor, DC were harvested, fixed, washed extensively, and used as APC in an IFN-γ ELISPOT assay where T cell clones are effectors. DC were added to an excess of T cells so that antigen was the limiting factor (see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000374#s4" target="_blank">Materials and Methods</a>). The mean number of spots produced by each clone was: D160 1-23 (228.4±39.3 to Mtb–infected DC, 19.6±6 to uninfected DC), D480 F6 (623.5±73.7 to Mtb–infected DC, 6.7±2.5 to uninfected DC), D454 E12 (453±52.4 to Mtb–infected DC, 13±4.4 to uninfected DC). Data have been normalized to the untreated control, and each bar reflects the mean±SEM of at least three experiments per clone (*p<0.05, **p<0.01 using two-tailed Student's t test compared to untreated controls, except where indicated). (C,D) DC were transduced with either empty vector or adenoviral ICP47 using Lipofectamine 2000. After 6–26 hours, DC were washed and infected with H37Rv-eGFP (C) or pulsed with antigen (D). Following overnight incubation, T cell clones were added and IFN-γ production was assessed by intracellular cytokine staining. The mean percentage of IFN-γ⁺ clones was: D160 1-23 (8.2±1.1 to Mtb–infected DC, 1.1±0.2 to uninfected DC), D480 F6 (46.4±3.9 to Mtb–infected DC, 1.5±0.4 to uninfected DC), D454 E12 (64±6 to Mtb–infected DC, 0.7±0.3 to uninfected DC). Each bar represents the mean±SEM of seven independent experiments.</p

The Mtb phagosome contains HLA-I loading accessory molecules.

<p>(A) DC were pulsed with H37Rv-eGFP for 20 minutes, washed, and incubated for 40 minutes. Phagosomal fractions were prepared as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000374#ppat-1000374-g003" target="_blank">Figure 3</a> and stained with the indicated antibodies (top panel). Intact DC were fixed, permeabilized, and stained with the indicated antibodies (bottom panel). Data are representative of three experiments. (B) Quantitative analysis of Mtb phagosomes over time. The percent positive number represents Overton cumulative histogram subtraction of the isotype control from the indicated stain. Each bar represents the mean±SEM from three experiments per timepoint.</p

The Mtb phagosome retains characteristics of an early endosome.

<p>(A) Representative figure showing organelle distribution after percoll separation of homogenate from Mtb–infected DC. The plasma membrane was labeled with a PE-conjugated antibody to HLA-II prior to homogenization and fluorescence was detected by fluorometry. For detection of ER, fractions were assessed for the presence of TAP1 and PDI by western blot. An enzymatic assay for β-hexosaminidase was used for detection of lysosomes. Finally, fractions were examined for the presence of H37Rv-eGFP by flow cytometry and quantified using a reference latex bead population. For flow cytometric analysis of Mtb phagosomes, the final 2 ml (fractions 23–28) of the gradient were pelleted, fixed, permeabilized, and stained with antibodies of interest. (B) Magnetic bead and Mtb phagosomes were gated based on FSC/SSC (not shown) and then on LAMP-1/HLA-I (beads) or LAMP-1/GFP (Mtb). Arrows indicate the gated population. Analysis of phagosome maturation on one hour LAMP-1^lo/−/HLA-I⁺ magnetic bead phagosomes (top panel), one hour LAMP-1⁺/HLA-I^lo/− magnetic bead phagosomes (second panel), overnight LAMP-1⁺ magnetic bead phagosomes (third panel), and overnight Mtb phagosomes (bottom panel). Plots include isotype staining (shaded histograms) as well as staining with the indicated antibody (red lines). The amplified HLA-I signal on the HLA-I-FITC gated events is due to the use of primary and secondary antibody combination, with which we routinely see up to a log shift in signal over conjugated primary. (C,D) Quantitative analysis of phagosomes over time. The percent positive number represents Overton cumulative histogram subtraction of the isotype control from the indicated stain. Each bar represents the mean±SEM of three experiments per timepoint.</p

Mtb proteins require retrotranslocation for presentation.

<p>(A,B) DC were treated with exoA or cycloheximide for one hour prior to infection with H37Rv-eGFP (A) or addition of CFP10 and CFP10_3–11 (B). DC were harvested, fixed, and assessed for their ability to stimulate T cell clones by IFN-γ ELISPOT as described. Each bar reflects the mean±SEM of at least three experiments. ND, not done. (C) DC were treated with exoA, exoA/PJ34, or BSA/PJ34 for one hour prior to infection with vaccinia virus expressing eGFP. After 16–18 hours, DC were harvested and GFP expression analyzed by flow cytometry. Data are representative of three experiments. (D,E) DC treated with exoA, BSA, exoA/PJ34, or BSA/PJ34 for one hour were subsequently infected with H37Rv-eGFP (D) or pulsed with antigen (E) overnight, harvested, fixed, and assessed for their ability to stimulate T cell clones by IFN-γ ELISPOT. Data are representative of two experiments. (F) DC were treated with exoA, exoA/PJ34, or BSA/PJ34 for one hour prior to infection with vaccinia virus expressing HIV p24. After 16–18 hours, DC were harvested, fixed and used to stimulate the HIV p24_306–316-specific CD8⁺ clone 16A7 in an IFN-y ELISPOT assay. Data are representative of two experiments.</p

HLA-I, loading machinery, and HLA-I:peptide complexes are present in highly pure Mtb phagosomes.

<p>(A) Phagosomes were isolated by percoll gradient or magnetic purification and prepared for electron microscopy as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000374#s4" target="_blank">Materials and Methods</a>. (B) Magnetic bead-isolated phagosomes were analyzed by flow cytometry to assess HLA-II-PE (plasma membrane) and H37Rv-eGFP fluorescence as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000374#s4" target="_blank">Materials and Methods</a> and <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000374#ppat-1000374-g006" target="_blank">Figure 6</a>. The events shown represent a small proportion of the population of phagosomes isolated and the experiment is representative of three experiments. (C) DC were pulsed with magnetically-labeled H37Rv-eGFP for 20 minutes, washed, and incubated for 18 hr. After magnetic separation of Mtb phagosomes, flow organellometry was performed as described previously. Data are representative of three experiments. (D) Magnetically-isolated Mtb phagosomes were freeze-thawed and tested for their ability to stimulate D160 1-23 CD8⁺ T cell clones in the absence of additional APC. IFN-γ production was measured using ELISPOT. Data are representative of two experiments.</p

Mtb phagosomes contain minimal contamination.

<p>(A) HLA-A2⁻ or HLA-A2⁺ DC were infected with H37Rv-eGFP for 20 minutes, washed, and incubated for an additional 40 minutes. HLA-A2⁻ DC were mixed with uninfected HLA-A2⁺ DC, homogenized, and homogenate separated using 27% percoll as described or pelleted without percoll separation. Phagosomes were stained with an antibody to HLA-A2. Shaded histograms represent isotype staining. Data are representative of three experiments. (B) HLA-A2⁻ or HLA-A2⁺ LCL were fixed, permeabilized, and stained with an antibody to HLA-A2. (C,D) Mtb phagosomes (C) or intact DC (D) were analyzed for the presence of cis- and trans-golgi markers GM130 and golgin-97, respectively. Data in C are representative of three experiments each after a 40 minute or overnight chase. Data in D are representative of two experiments.</p

Nonclassical CD8⁺ T-cell clones predominate in TB-uninfected individuals.

a<p>These frequencies were previously reported <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000407#pbio.1000407-Lewinsohn2" target="_blank">[4]</a>.</p><p>Abbreviations: N.D., not done.</p

MR1-restricted recognition of Mtb-infected cells is TAP-independent.

<p>DCs autologous to D454 and expressing HLA-B08 were transduced with either a control adenoviral vector or adenoviral ICP47 using lipofectamine 2000. After 16 h, DCs were washed and either left uninfected, infected with Mtb, or pulsed with HLA-B08 specific peptide CFP10_3–11. Following overnight incubation, T cells were added (10,000) to DCs (25,000/well) and IFN-γ production was assessed by ELISPOT. Results are representative of three independent assays. No responses were detected from T cells incubated with uninfected DCs with or without adenoviral vectors. Error bars represent the mean and standard error from duplicate wells.</p

MR1 presents a protein-containing antigen from the mycobacterial cell wall.

<p>(A) CFP or CW from the Mtb strain H37Rv were added (5 µg/ml) to DCs (25,000/well) for 1 h prior to the addition of one of 21 NC clones (5,000/well) followed by IFN-γ ELISPOT assay. (B) DCs (25,000) loaded with CW overnight were incubated with anti-MR1 blocking antibody (clone 26.5) or a mouse IgG2a isotype control (both at 5 µg/ml) for 1 h prior to the addition of T-cell clones (10,000/well). (C) dCW from Mtb was treated with proteases (subtilisin, trypsin, chymotrypsin, pronase, Glu-C) and added (5 µg/ml) to DCs (25,000/well) for 1 h before the addition of 21 NC clones (5,000/well) that were tested for their ability to produce IFN-γ in an ELISPOT assay. Reversed phase- high performance liquid chromatography (RP-HPLC) chromatogram analyses were used to confirm the inactivation of proteases. No responses were detected in the absence of DCs. (D) DCs were infected with <i>S. typhimurium</i>, <i>L. monocytogenes</i>, <i>and S. aureus</i> for 1 h with a calculated moi of 145, 6, and 15, respectively. DCs were washed, antibiotics added, and DCs (25,000) were incubated with three different Mtb-reactive MAIT-cell clones (10,000/well) that were tested for their ability to produce IFN-γ in an ELISPOT assay. Results shown are similar to a minimum of three independent experiments where <i>S. typhimurium</i>, <i>L. monocytogenes</i>, <i>and S. aureus</i> were tested at a variety of moi ranging from 5 to 150.</p

LDA of Mtb-reactive CD8⁺ T-cell clones.

<p>Scatter plot demonstrating the proportion of NC restricted CD8⁺ T-cell clones obtained from individuals in the active, LTBI, and uninfected groups. Each symbol represents the average frequency from all clones screened from an individual donor (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000407#pbio-1000407-t001" target="_blank">Table 1</a>), which was categorized as NC restricted. The nonparametric Mann Whitney one-tailed <i>t</i>-test was used to assess statistical significant differences between groups. Significant differences were detected between active and uninfected groups (<i>p</i> = 0.0043) between the active and LTBI groups (<i>p</i> = 0.0411), but not between the LTBI and uninfected groups (<i>p</i> = 0.3362).</p