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Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses

Abstract

To tackle the complexity of cross-reactive and pathogen-specific T cell responses against related Salmonella serovars, we used mass cytometry, unbiased single-cell cloning, live fluorescence barcoding, and T cell–receptor sequencing to reconstruct the Salmonella-specific repertoire of circulating effector CD4+ T cells, isolated from volunteers challenged with Salmonella enterica serovar Typhi (S. Typhi) or Salmonella Paratyphi A (S. Paratyphi). We describe the expansion of cross-reactive responses against distantly related Salmonella serovars and of clonotypes recognizing immunodominant antigens uniquely expressed by S. Typhi or S. Paratyphi A. In addition, single–amino acid variations in two immunodominant proteins, CdtB and PhoN, lead to the accumulation of T cells that do not cross-react against the different serovars, thus demonstrating how minor sequence variations in a complex microorganism shape the pathogen-specific T cell repertoire. Our results identify immune-dominant, serovar-specific, and cross-reactive T cell antigens, which should aid in the design of T cell–vaccination strategies against Salmonella.

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Change history

  • 12 March 2019

    In the version of this article initially published, the first affiliation lacked ‘MRC’; the correct name of the institution is ‘MRC Weatherall Institute of Molecular Medicine’. Two designations (SP110Y and ST110H) were incorrect in the legend to Fig. 6f,h,i. The correct text is as follows: for panel f, “...loaded with either the CdtB(105–125)SP110Y (DRB4*SP110Y) or the CdtB(105–125)ST110H (DRB4*ST110H) peptide variants...”; for panel h, “...decorated by the DRB4*SP110Y tetramer (lower-right quadrant), the DRB4*ST110H (upper-left quadrant)...”; and for panel i, “...stained ex vivo with DRB4*SP110Y, DRB4*ST110H...”. In Fig. 8e, the final six residues (LTEAFF) of the sequence in the far right column of the third row of the table were missing; the correct sequence is ‘CASSYRRTPPLTEAFF’. In the legend to Fig. 8d, a designation (HLyE) was incorrect; the correct text is as follows: “(HlyE?).” Portions of the Acknowledgements section were incorrect; the correct text is as follows: “This work was supported by the UK Medical Research Council (MRC) (MR/K021222/1) (G.N., M.A.G., A.S., V.C., A.J.P.),...the Oxford Biomedical Research Centre (A.J.P., V.C.),...and core funding from the Singapore Immunology Network (SIgN) (E.W.N.) and the SIgN immunomonitoring platform (E.W.N.).” Finally, a parenthetical element was phrased incorrectly in the final paragraph of the Methods subsection “T cell cloning and live fluorescence barcoding”; the correct phrasing is as follows: “...(which in all cases included HlyE, CdtB, Ty21a, Quailes, NVGH308, and LT2 strains and in volunteers T5 and T6 included PhoN)...”. Also, in Figs. 3c and 4a, the right outlines of the plots were not visible; in the legend to Fig. 3, panel letter ‘f’ was not bold; and in Fig. 8f, ‘ND’ should be aligned directly beneath DRB4 in the key and ‘ND’ should be removed from the diagram at right, and the legend should be revised accordingly as follows: “...colors indicate the HLA class II restriction (gray indicates clones for which restriction was not determined (ND)). Clonotypes are grouped on the basis of pathogen selectivity (continuous line), protein specificity (dashed line) and epitope specificity; for ten HlyE-specific clones (pixilated squares), the epitope specificity was not determined...”. The errors have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

This work was supported by the UK Medical Research Council (MRC) (MR/K021222/1) (G.N., M.A.G., A.S., V.C., A.J.P.), Cancer Research UK (CRUK) (C399/A2291) (V.C.), the NIHR Clinical Research Network Thames Valley (A.J.P.), the Oxford Biomedical Research Centre (A.J.P., V.C.), the Bill & Melinda Gates Foundation (OPP1084259) (A.J.P.), the European Vaccine Initiative (PIM) (A.J.P.), and core funding from the Singapore Immunology Network (SIgN) (E.W.N.) and the SIgN immunomonitoring platform (E.W.N.). G.D. is supported by The Wellcome Trust. We thank C. Waugh and the WIMM FACS facility for assistance with cell sorting, and T. Rostron for assistance with next-generation sequencing. The DRB4 tetramers were provided by B. Kwok and I.-T. Chow, from the Tetramer Core Laboratory at the Benaroya Research Institute at Virginia Mason.

Author information

G.N. conceived and designed the study, processed the samples, performed and supervised the experiments, analyzed the data, and wrote the manuscript. P.K. processed the samples, performed experiments, and analyzed the data. L.H., P.d.H., L.P.-L., L.S., and M.S. assisted with experiments. A.A. designed and performed bacteria–macrophage coculture experiments. M.R. and D.M.S.P. optimized and performed TCR-repertoire experiments and analysis. K.W.W.T., E.B., M.T.W., and E.W.N. developed the metal-conjugated antibody panels, coordinated and performed the mass cytometry experiments, and provided assistance with the analysis of mass cytometry experiments. A.J.P. conceived the development of the human-challenge model and directed the clinical trial. H.D. and M.M.G. designed and directed the clinical trial. D.C., C.J., and C.J.B. coordinated the clinical trial and sampling. C.J., H.T.-B., and H.B.J. coordinated sampling and processed samples. L.R.O. designed peptide pools containing overlapping peptides. S.B., G.D., D.B., and D.P. provided reagents. G.N., M.A.G., A.S., V.C., and A.J.P. coordinated the study. V.C. conceived and designed the study, edited the manuscript, and supervised performing of experiments. All authors discussed the results and commented on the manuscript.

Correspondence to Giorgio Napolitani.

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Integrated supplementary information

Supplementary Figure 1 Characterization of Ki67+ cells accumulating during enteric fever.

(a)Gating strategy to identify CD4+ and CD4+Ki67+ cells in Mass Cytometry experiments. Frequency of Cluster 19 cells within Ki67+ (b) and total CD4+ T cells (c) at different time points after infection (n = 6). (b) Friedman Test p = 0.0147, Dunn’s Multiple Comparison Test D0 vs D4, D28, D90 p = ns, D0 vs EF p = 0.027. (c)Friedman Test p = 0.0159, Dunn’s Multiple Comparison Test D0 vs D4, D28, D90 p = ns, D0 vs EF p = 0.0247. (d) Total Ki67+ events (grey) and Cluster 19 events (red) across all samples were concatenated and expression of 20 markers against CD38 in the distinct populations is shown.

Supplementary Figure 2 CCR7CD38+CD4+ cells are enriched in Ki67+ accumulating during enteric fever.

(a) Expression of CCR7 and CD38 in the 20 distinct clusters identified by PhenoGraph analysis. (b) Proportion of PhenoGraph clusters within Ki67+ CD38+CCR7- cells at the peak of Ki67+ cell accumulation. (c) Frequency of Ki67+ CD38+CCR7- cells (Friedman Test p = 0.0130, Dunn’s Multiple Comparison Test D0 vs D4, D28, D90p = ns, D0 vs EF p = 0.0139) and of KI67 + cells non comprised within CD38+CCR7- cells over time in challenged volunteers (n = 6) (Friedman Test p = 0.23, Dunn’s Multiple Comparison Test D0 vs D4, EF, D28, D90 p = ns). Box extends from the 25th to the 75th percentile and whiskers from the minimum to the maximum value; line indicates median.

Supplementary Figure 3 Accumulation of CD4+CD38+CCR7 in whole blood of volunteers with enteric fever

(a) Identification of CD4+CD38+CCR7- cells during enteric fever by Multicolour Flow Cytometry in whole blood from a representative volunteer challenged with S. Typhi, and one challenged with S. Paratyphi A. (b) Accumulation of CD38+CCR7- cells after diagnosis in volunteers challenged with S. Typhi and Paratyphi A who developed (Diagnosed) but not in those who did not develop enteric fever (Not Diagnosed). In challenged volunteers not diagnosed blood was collected 14 days after challenge (D14). Friedman Multi comparison Test p = 0.006 (S. Typhi), p < 0.0001 (S. Paratyphi). Dunn’s Multiple Comparison Test ED vs D0, p = 0.0065 (Typhi, n = 9); p = 0.0002 (S. Paratyphi A, n = 9). Box extends from the 25th to the 75th percentile and whiskers from the minimum to the maximum value; line indicates median.

Supplementary Figure 4 Gating strategy for live fluorescence barcoding of T cell clones

Shown is an example with four live fluorescent dyes. Cell were labelled with 9 combinations of three distinct dilution of Violet and Far red dyes. Cells with each of the nine cluster were labelled with 6 combinations of 4 distinct dilutions of CFSE and and 3 of CMTMR orange dyes. Dilutions used for adjacent clusters across the 640-670 axis were labelled with alternate dilutions of CFSE and CMTMR Orange (as shown in the overlaid plots) in order to reduce spill-over in case of suboptimal separation between clusters across the channel-dye combination with the lowest stain index.

Supplementary Figure 5 Increased frequency of HlyE- and CdtB- specific T cells in volunteers diagnosed with enteric fever

(a) Frequency of HlyE, CdtB and Flu specific T cell responses 28 days after challenge measured by IFN-g ELISPOT in volunteers challenged with S. Typhi or S. Paratyphi A who developed (Diagnosed, D, n = 12) or did not develop (Not Diagnosed, ND, n = 9)) enteric fever compared to uninfected controls (HC. n = 10). Freshly isolated PBMC were rested overnight and incubated with 5μg/ml of HlyE or CdtB peptide pools, or with inactivated seasonal influenza vaccine (Flu). Mann Witney two tailed t-test. * = p < 0.05; ** = p < 0.005. Box extends from the 25th to the 75th percentile and whiskers from the minimum to the maximum value; line indicates median.

Supplementary Figure 6 CdtB-specific clones help macrophages limit bacterial spread

(a) Monocyte derived macrophages (MF) were differentiated for 5 days in the lower chamber of 24 well transwell plates. At day 5 a pool of 3 CdtB specific clones (T) was added to the upper well in the presence or absence of CdtB peptide pool (CdtB). After O.N. incubation, upper well was removed, macrophages were washed, infected with S. Typhimurium (LT2 strain) for 30 m, washed again and incubated with Gentamicin (30 mg/ml) to limit bacterial overgrowth. 2 h after infection cell culture supernatant was plated in agar plates and colonies counted after over night culture. Indicated is the percentage of bacterial growth compared to macrophages alone (n = 6, Friedman test (p = 0.0008) with Dunn’s multiple comparisons test (control vs T + CdtB p = 0.0169). Box extends from the 25th to the 75th percentile and whiskers from the minimum to the maximum value; line indicates median. (b) CFU after O.N. culture of macrophage supernatant in agar plate in one representative experiment.

Supplementary Figure 7 Increased frequency of CdtB, HlyE, and PhoN T cell responses after diagnosis with enteric fever

(a) Frequency of HlyE, CdtB, and Flu specific T cell responses at baseline and 28 days after challenge measured by IFN-g ELISPOT in frozen PBMC from volunteers challenged with S. Typhi or S. Paratyphi A who developed (n = 19) enteric fever (Wilcoxon matched-pairs signed rank test). (b) Frequency of HlyE, CdtB, PhoN and Flu specific T cell responses in HLADRB4 + and HLADRB4- volunteers 28 days after challenge (Mann Whitney test two-tailed p value). (c) Frequency of PhoN specific T cell responses at baseline and 28 days after challenge measured by IFN-g ELISPOT in frozen PBMC from volunteers challenged with S. Typhi or S. Paratyphi A who developed (n = 19) enteric fever and in HLADRB4+ and HLADRB4- individuals. ELISPOT analysis done on the same frozen samples as in panel a and b.

Supplementary Figure 8 Clonal expansion of Salmonella-specific effector T cells

(a) Rarefaction curve describing the estimated diversity of the CDR3β repertoire of CD38+CCR7- and CD38-CCR7- subsets in volunteers P1 and T4. Dots between continuous and dashed curves indicate the number of TCRs identified within each sample. Number of cells probed: P1 CD38+CCR7- = 5087 cells, CD38-CCR7- = 1.15e105 cells; T4 CD38+CCR7- = 9130 cells, CD38-CCR7- = 1.3e105 cells. (b) Pathogen selectivity, antigen specificity, restriction, CDR3α and CDR3β sequence of clones isolated from volunteer P1. Starred(*) sequences were identified also in the polyclonal analysis. (c) Pie Chart depicting the frequency of CDR3β sequences within the polyclonal repertoire of CD38+CCR7- cells (5087 cells probed) from T4, highlighted are the CDR3β sequences identified in the isolated clones. (d) Frequency of CDR3β within the polyclonal repertoire of CD38+CCR7- cells and CD38-CCR7- cells in volunteer P1 (1.15e105 cells probed). Red circles represent CDR3β sequences identified in the isolated clones.

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Further reading

Fig. 1: Mass cytometry identification of effector CD4+ T cells responding to Salmonella infection.
Fig. 2: CD38+CCR7CD4+ T cells contain a homogeneous population of IFNγ- and MIP-1β-producing cells.
Fig. 3: Analysis of libraries of CD38+CCR7 T cell clones and fluorescence barcoding to dissect the antigen-specific repertoire of effector CD4+ T cells.
Fig. 4: Cross-reactivity of Salmonella-specific CD4+ T cell clones against different Salmonella serovars.
Fig. 5: HlyE and CdtB are S. Typhi– and S. Paratyphi A–specific immunodominant T cell antigens.
Fig. 6: Sequence-dependent recognition of different Salmonella serovars by CdtB-specific T cell clones.
Fig. 7: Characterization of the specificity of T cell clones cross-reactive against nontyphoidal Salmonella.
Fig. 8: Clonal expansion of Salmonella-specific effector T cells.
Supplementary Figure 1: Characterization of Ki67+ cells accumulating during enteric fever.
Supplementary Figure 2: CCR7CD38+CD4+ cells are enriched in Ki67+ accumulating during enteric fever.
Supplementary Figure 3: Accumulation of CD4+CD38+CCR7 in whole blood of volunteers with enteric fever
Supplementary Figure 4: Gating strategy for live fluorescence barcoding of T cell clones
Supplementary Figure 5: Increased frequency of HlyE- and CdtB- specific T cells in volunteers diagnosed with enteric fever
Supplementary Figure 6: CdtB-specific clones help macrophages limit bacterial spread
Supplementary Figure 7: Increased frequency of CdtB, HlyE, and PhoN T cell responses after diagnosis with enteric fever
Supplementary Figure 8: Clonal expansion of Salmonella-specific effector T cells