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. 2022 Sep 5;219(9):e20210828.
doi: 10.1084/jem.20210828. Epub 2022 Aug 26.

CD8 coreceptor engagement of MR1 enhances antigen responsiveness by human MAIT and other MR1-reactive T cells

Michael N T Souter  1 , Wael Awad  2 , Shihan Li  1 , Troi J Pediongco  1 , Bronwyn S Meehan  1 , Lucy J Meehan  1 , Zehua Tian  1 , Zhe Zhao  1 , Huimeng Wang  1   3 , Adam Nelson  1 , Jérôme Le Nours  2 , Yogesh Khandokar  2 , T Praveena  2 , Jacinta Wubben  2 , Jie Lin  1 , Lucy C Sullivan  1 , George O Lovrecz  4 , Jeffrey Y W Mak  5 , Ligong Liu  5 , Lyudmila Kostenko  1 , Katherine Kedzierska  1 , Alexandra J Corbett  1 , David P Fairlie  5 , Andrew G Brooks  1 , Nicholas A Gherardin  1 , Adam P Uldrich  1 , Zhenjun Chen  1 , Jamie Rossjohn  2   6 , Dale I Godfrey  1 , James McCluskey  1 , Daniel G Pellicci  1   7 , Sidonia B G Eckle  1
Affiliations

CD8 coreceptor engagement of MR1 enhances antigen responsiveness by human MAIT and other MR1-reactive T cells

Michael N T Souter et al. J Exp Med. .

Abstract

Mucosal-associated invariant T (MAIT) cells detect microbial infection via recognition of riboflavin-based antigens presented by the major histocompatibility complex class I (MHC-I)-related protein 1 (MR1). Most MAIT cells in human peripheral blood express CD8αα or CD8αβ coreceptors, and the binding site for CD8 on MHC-I molecules is relatively conserved in MR1. Yet, there is no direct evidence of CD8 interacting with MR1 or the functional consequences thereof. Similarly, the role of CD8αα in lymphocyte function remains ill-defined. Here, using newly developed MR1 tetramers, mutated at the CD8 binding site, and by determining the crystal structure of MR1-CD8αα, we show that CD8 engaged MR1, analogous to how it engages MHC-I molecules. CD8αα and CD8αβ enhanced MR1 binding and cytokine production by MAIT cells. Moreover, the CD8-MR1 interaction was critical for the recognition of folate-derived antigens by other MR1-reactive T cells. Together, our findings suggest that both CD8αα and CD8αβ act as functional coreceptors for MAIT and other MR1-reactive T cells.

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Conflict of interest statement

Disclosures: J.Y.W. Mak, L. Liu, A.J. Corbett, D.P. Fairlie, Z. Chen, J. Rossjohn, J. McCluskey, and S.B.G. Eckle reported a patent (WO/2015/149130) with royalties paid by Immudex and licensed to the NIH Tetramer Core Facility. L. Liu, A.J. Corbett, D.P. Fairlie, J. Rossjohn, J. McCluskey, and S.B.G. Eckle reported a patent (WO/2014/005194) with royalties paid by Immudex and licensed to the NIH Tetramer Core Facility. D.I. Godfrey reported a patent to PROVAU2022900574 pending. No other disclosures were reported.

Figures

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Graphical abstract
Figure 1.
Figure 1.
Adult peripheral blood MAIT cells predominately express CD8, and the canonical CD8 binding site is conserved between MHC-I and MR1. (A) Gating strategy for assessing coreceptor usage by MAIT and non-MAIT T cells from peripheral blood identified using MR1-5-OP-RU tetramer. (B) Coreceptor usage by MAIT cells among 11 healthy donors showing the frequency of each subset (CD4, DN, DP and CD8) as a percentage of total MAIT cells. (C–E) The frequency of CD8αα and CD8αβ usage as a percentage of CD8 SP MAIT cells, DP MAIT cells, or CD8+ non-MAIT T cells, respectively. (F and G) Geometric MFI (gMFI) of CD8α and CD8β antibody staining of CD8αα+ and CD8αβ+ MAIT cells compared to non-MAIT CD8αβ+ T cells. (B–G) Data from 11 healthy blood donors were assessed in two independent experiments. (H) Alignment of residues 211–235 (Q223 highlighted in red) of the α3-domains of human and mouse MHC-Ia/b molecules with human MR1, annotated with residues engaged in hydrogen bonds (highlighted in blue) between both the T cell proximal (CD8β or CD8α1) and distal (CD8α2) CD8 subunits, respectively. Indicated residue numbers apply to MR1, whereby HLA-A*02:01 residue numbers are those of MR1 plus 3. CD8 subunit positions are highlighted in red on cartoons of CD8–MHC-I. Interactions of CD8 with MHC-I molecules were identified with PDBsum (Laskowski et al., 2018) using published crystal structures with PDB IDs; 1AKJ (Gao et al., 1997), 3QZW (Shi et al., 2011), 1BQH (Kern et al., 1998), 3DMM (Wang et al., 2009), and 1NEZ (Liu et al., 2003). Statistical significance was determined using a Friedman test with Dunn’s multiple comparison (B and F) or Wilcoxon signed-rank test (G).
Figure S1.
Figure S1.
High sequence conservation of MR1 in the putative CD8 binding site and validation of reporter cell lines and recombinant proteins. (A) Protein sequence alignment of a segment of the MR1 α3-domain from common mammals, including human (Homo sapiens), monkey (Macaca fascicularis), pig (Sus scrofa), cattle (Bos taurus), rat (Rattus norvegicus), and mouse (Mus musculus) using UniProt accession numbers Q95460, A0A2K5W2L6, A0A5G2R2T2, C1ITJ8, O19477, and Q8HWB0, respectively. The conserved residue Q223 is highlighted in red, and residues not conserved with human MR1 are highlighted in black. (B) Histograms comparing gMFI of parental (CD8 deficient), CD8αα transduced (+CD8αα), and CD8α- and CD8β-transduced (+CD8αβ) cells stained with anti-CD8α/β conjugated antibodies. (C) MR1-5-OP-RU tetramer staining of parental or CD8 transduced SKW-3.β2mnull cells described above. (D) As above, comparing MR1 and HLA tetramer staining and displaying gMFI. Data are representative of two experiments. (E) WT and CD8-null MR1 monomers folded with 5-OP-RU or 6-FP (5 μg each) analyzed by SDS-PAGE (15% polyacrylamide) under reducing conditions using 1 mM dithiothreitol (DTT) alongside a molecular weight marker (BM) with a protein range of 10–220 kD. Proteins were stained using Coomassie Blue R-250 dye. (F) WT and CD8-null MR1 monomers folded with 5-OP-RU or 6-FP (5 μg each) mixed with streptavidin (SAv; 5 μg) and analyzed by SDS-PAGE (12% polyacrylamide) under non-reducing conditions with SAv alone, or MR1-6-FP and MR1-5-OP-RU monomers alone alongside a molecular weight marker. (G) WT and CD8-null MR1-5-OP-RU (black) or -6-FP (gray) tetramer staining of a MAIT TCR (A-F7) expressing Jurkat cell line. Data are representative of two experiments. (H) Soluble CD8αα (2 μg) analyzed by SDS-PAGE (12% polyacrylamide) under reducing (1 mM DTT, +DTT) and non-reducing (−DTT) conditions alongside a molecular weight marker (BM).
Figure 2.
Figure 2.
MR1 binds to CD8 in a manner concordant with MHC-I. (A) gMFI of CD8αα or CD8αβ expressing cells stained with titrating doses of MR1 (MR1-5-OP-RU) or MHC-I (HLA-A*02:01-NLV, HLA-B*08:01-FLR, HLA-C*06:02-TRAT and HLA-G*01:01-RII) tetramers or streptavidin (SAv) control as determined by flow cytometry. (B) Dissociation of MR1-5-OP-RU and HLA-A*02:01-NLV tetramers from CD8αα or CD8αβ expressing cells over 120 min, measured by flow cytometry. Data points are mean values fitted with a nonlinear regression line (least squares) and 95% CI bands. (C) Binding of α3-domain MR1-Ac-6-FP mutant tetramers to CD8αα (left) and CD8αβ (right) expressing cell lines, displayed as fold change compared to WT MR1-Ac-6-FP tetramer (gMFI). Green underlay defines a ±0.5-fold change from baseline. Schematic representation of MR1-5-OP-RU (PDB ID; 6PUC; Awad et al., 2020) with a color-coded α3-domain Connolly surface overlay of key residues. (D) Histograms depicting 5-OP-RU–, 6-FP–, or Ac-6-FP–folded WT or Q223A, E224K mutant (MT) MR1 tetramer binding to CD8αα and CD8αβ expressing cells. (E) Affinity plot (top right panel) and sensorgrams (all other panels) of the WT or CD8-null MR1-Ac-6-FP (left panels), HLA-A*02:01-NLV (middle panels), and CD1d (bottom right panel) interactions with immobilized CD8αα, determined by SPR, where the response is measured in resonance units (RU). Data are representative of two (A, C, and E) or three (B and D) independent experiments.
Figure 3.
Figure 3.
Crystal structure of the CD8αα–MR1-Ac-6-FP ternary complex. (A) Ribbon diagram of the X-ray crystal structure of the CD8αα–MR1-Ac-6-FP complex. The MR1 and β2m molecules are colored white and pale cyan, respectively, and Ac-6-FP is shown as green sticks. The CD8α1 and CD8α2 subunits are colored pale green and wheat, respectively. Displayed are two orientations of the complexes, involving a 45° rotation along the y axis. (B) Surface representation of the CD8αα–MR1-Ac-6-FP complex in the same colors and orientation (right panel) as in A. The lower left panel displays the footprint of CD8αα on MR1-β2m, rotated clockwise by 90° along the y axis; the lower right panel displays the footprint of MR1-β2m on CD8αα, rotated counter-clockwise by 90° along the y axis. The interaction regions are highlighted with exchanged colors and the H-bond/salt bridge/vdw forming residues are indicated, with H-bond or salt bridge forming residues bolded and underlined. Residues that contact both CD8α1 and CD8α2 subunits are in red. Residues mutated in CD8-null MR1 are highlighted as black dotted lines. (C–F) Close-up presentation of the molecular contacts at the interface between CD8αα and MR1-Ac-6-FP. Selected hydrogen bonds (black dashed lines), salt bridges (red dashed lines), and vdw interactions (orange dashed lines) between the β-sheet base of the MR1 antigen presentation cleft, β2m and the CD8α1 subunit (C), and between the MR1-α3 domain and the CD81α subunit (D) or the CD8α2 subunit (E), as well as between the MR1 CD loop with residues of both subunits of CD8αα (F) are shown. The residues of MR1 and β2m are presented as white and pale cyan sticks respectively, whereas the interacting residues of CD8α1 and CD8α2 are displayed as pale green and wheat sticks, respectively.
Figure S2.
Figure S2.
Electron density maps of the ligand Ac-6-FP and important interfaces in the crystal structure of the CD8αα–MR1-Ac-6-FP ternary complex. (A) Ribbon diagram of the X-ray crystal structure of the CD8αα–MR1-Ac-6-FP complex. (B–F) Electron density maps (2Fo-Fc; blue mesh contoured at 1σ) of selected regions of the MR1-Ac-6-FP interface with CD8αα, each highlighted with a differently colored box in panel A: the MR1-β2m interface with the CD8α1 subunit (B), the MR1 interacting regions of the CD8α1 subunit (C), the MR1 CD loop (D), the MR1 interacting regions of the CD8α2 subunit (E), and Ac-6-FP (F).
Figure S3.
Figure S3.
Structural comparison of the ternary complexes of CD8αα–MR1-Ac-6-FP and CD8αα–HLA-A*02:01. (A and D) Docking of CD8αα (surface presentation) on the side of MR1-Ac-6-FP (A) and HLA-A*02:01-peptide (PDB: 1AKJ) (D; ribbon presentation). (B and E) Surface presentation showing the footprint of CD8αα on MR1-Ac-6-FP (B) and HLA-A*02:01-peptide (E). (C and F) Selected H-bond and salt-bridge interactions (black dashed lines) between CD8αα and the CD loops of MR1 (C) and HLA-A*02:01 (analysis of the crystal structure with PDB ID 1AKJ [Gao et al., 1997] as per the criteria in Table S2; F), respectively. The two complexes were aligned via the α1/α2 domains of the MHC-I–like/MHC-I heavy chains in PyMOL. The CD8αα–MR1-Ac-6-FP complex is colored as in Fig. 4. The CD8αα–HLA-A*02:01-peptide complex is colored as follows: HLA-A*02:01, sky blue; β2m, slate blue; CD8α1, teal; CD8α2, light pink. (G) Superposition of the CD8αα–HLA-A*02:01-peptide and CD8αα–MR1-Ac-6-FP structures. Arrows illustrate the CD8αα rotation around the center of mass of the MR1/HLA-A*02:01 molecules. (H) Zoomed view of the interaction between CD8αα and the CD loops in the α3 domains of MR1 and HLA-A*02:01. (I) Superposition of the CD8αα molecules (ribbon presentation) in both MR1-Ac-6-FP and HLA-A*02:01-peptide complex structures. The right panel shows the bottom view of various CD8αα–CDR-like loops. The CD8αα molecules in panel G were aligned using PyMOL. (J) Alignment of residues 179–270 of the α3-domains of human MR1 and HLA-A*02:01, annotated with residues engaged in hydrogen bonds (highlighted in blue) between both the T cell proximal (CD8α1) and distal (CD8α2) CD8 subunits. Indicated residue numbers apply to MR1, whereby HLA-A*02:01 residue numbers are those of MR1 plus 3. Interactions of CD8 with the HLA-A*02:01 molecule in the published crystal structure with PDB ID 1AKJ (Gao et al., 1997) were identified as per the criteria in Table S2.
Figure 4.
Figure 4.
CD8–MR1 interactions enhance MR1 tetramer binding to MAIT cells and slow MR1 tetramer dissociation kinetics. (A) MAIT cells identified using WT MR1-5-OP-RU tetramers from PBMCs of human healthy donors and gated based on coreceptor usage. (B) Cumulative data for WT tetramer staining intensity of MAIT cell coreceptor subsets (10 donors for CD4+, 11 donors for all other subsets). (C) Comparison of WT tetramer staining intensity of CD8− and CD8+ MAIT cells in individual donors. (D) Gating strategy for defining low, intermediate, and high CD8α expression by CD8+ MAIT cells and cumulative data comparing WT tetramer staining intensity of CD8α+ MAIT cells with mean and SD value. (E) MAIT cells stained with titrating amounts of WT or CD8-null MR1-5-OP-RU or MR1-6-FP tetramers. (F) Cumulative data of WT and CD8-null tetramer staining intensity for MAIT cell coreceptor subsets. (G) Cumulative data (in triplicate) of WT and CD8-null tetramer dissociation over time from CD8 SP or DN MAIT cells from healthy blood donors. A nonlinear regression line (least squares) and 95% CI interval bands are fitted. (A–D) Data are from the same 11 healthy blood donors in Fig. 1, recorded from two independent experiments. kfast, fast rate constant; kslow, slow rate constant. (E–G) Data are from 12 additional healthy blood donors from three independent experiments. Statistical significance was determined using a Kruskal–Wallis test (B), Wilcoxon signed-rank test (C), Friedman test with Dunn’s multiple comparison (D), or a two-way ANOVA with Sidak's multiple comparisons test (F).
Figure S4.
Figure S4.
MAIT cell coreceptor subsets stain similarly with anti-CD3 and CD8-null MR1-5-OP-RU tetramer, validation of MR1 expression by reporter cell lines and readout for MAIT cell responses, and CD8 dependency of MAIT cell coreceptor subset responses. (A) CD3 expression (gMFI) of MAIT cells identified using MR1-5-OP-RU tetramer and segregated based on coreceptor expression as part of experiments shown in Figs. 1 and 4. (B) CD3 expression (gMFI) of CD8+ MAIT cells identified using MR1-5-OP-RU tetramer and segregated based on anti-CD8α antibody fluorescence (low, intermediate, high) as part of experiments shown in Fig. 4. (C) Cumulative data for CD8-null MR1-5-OP-RU tetramer staining intensity of MAIT cell coreceptor subsets (10–11 donors) shown in Fig. 4. Data are from two independent experiments. Statistical significance was determined using a Kruskal–Wallis test. (D) Histograms comparing the gMFI of MR1-deficient (MR1null), WT MR1 (MR1null+MR1), mutant CD8-null MR1 (MR1null+CD8-null MR1), and mutant MR1-K43A (MR1null+MR1-K43A) overexpressing C1R cells. (E) Percentage of IL-17A–producing MAIT cells in response to 10 nM 5-OP-RU in the presence of MR1 deficient (C1R.MR1null) cells or WT MR1 expressing (C1R.MR1null+MR1) cells. Mean and SD are displayed. (F and G) Percentage of TNF- or IFNγ-producing MAIT cells by individual donors in response to WT MR1 expressing C1R cells (C1R.MR1null+MR1) pulsed with 1,000 pM 5-OP-RU. (H and I) Percentage of TNF- or IFNγ-producing MAIT cell coreceptor subsets in response to WT or CD8-null MR1 expressing C1R cells pulsed with titrating doses of 5-OP-RU. (J) Comparison of TNF- and IFNγ-producing DN, CD8αα+ and CD8αβ+ MAIT cells in response to CD8-null MR1 expressing C1R cells pulsed with titrating doses of 5-OP-RU. Data are normalized to the maximum response for each MAIT cell subset. (H–J) Mean, SD and nonlinear regression line (least squares) are displayed. Statistical significance was determined using a Friedman test with Dunn’s multiple comparison (F and G).
Figure 5.
Figure 5.
CD8–MR1 interactions enhance antigen-dependent MAIT cell responses. (A) MAIT cells identified using surrogate markers CD161 and TRAV1-2 (left plots), and analysis of coreceptor usage and cytokine production (TNF and IFNγ) of unstimulated and 5-OP-RU stimulated MAIT cells (middle and right plots). (B and C) Percentage of TNF- or IFNγ-producing MAIT cells in response to 10 nM 5-OP-RU in the absence of C1R cells, or in the presence of MR1 deficient (C1R.MR1null) or WT MR1 expressing (C1R.MR1null+MR1) C1R cells. Mean and SD are displayed. (D and E) Percentage of TNF- or IFNγ-producing MAIT cell coreceptor subsets in response to WT MR1 expressing C1R cells (C1R.MR1null+MR1) pulsed with titrating doses of 5-OP-RU. Mean, SD, and nonlinear regression line (least squares) are displayed. (F and G) Percentage of TNF- or IFNγ-producing MAIT cells by individual donors in response to WT MR1 expressing C1R cells (C1R.MR1null+MR1) pulsed with 100 pM 5-OP-RU (∼EC50 dose). (H and I) Percentage of TNF- or IFNγ-producing MAIT cells, comparing the response in individual donors to WT or CD8-null MR1 expressing C1R cells (C1R.MR1null+MR1 or C1R.MR1null+MR1 CD8-null) pulsed with titrating doses of 5-OP-RU. (J and K) As above, comparing the percentage of TNF- or IFNγ-producing DN or CD8 SP MAIT cells. (B–J) Data are from 12 healthy blood donors from three independent experiments. Statistical significance was determined using a Friedman test with Dunn’s multiple comparison (F and G) or a two-way ANOVA with Sidak’s multiple comparisons test (H–K).
Figure S5.
Figure S5.
Expanded MR1-6-FP–reactive T cells from human PBMCs respond in a CD8 dependent manner, and splenic CD8+ MR1-reactive T cells are reliant on CD8 engagement for recognition of MR1 tetramers. (A) Gating strategy for sorting of enriched MR1-6-FP tetramer+ T cells (Post-enrichment) and verification of antigen reactivity after in vitro expansion (Post-expansion). (B) CD8α expression of expanded MR1-6-FP–reactive T cells from up to 12 healthy donors examined in Fig. 6. (C and D) Frequencies of expanded TRAV1-2− or TRAV1-2+ T cells that retain MR1-6-FP or -5-OP-RU tetramer reactivity post-expansion as part of experiments shown in Fig. 6. (E) Concentrations of cytokines secreted into culture supernatant by mixed TRAV1-2+/− expanded T cells from four healthy donors after stimulation with PMA/ionomycin (18 h). (F) CD8α expression of expanded MR1-6-FP–reactive T cells from nine healthy donors. (G and H) Frequencies of expanded TRAV1-2− or TRAV1-2+ T cells that retain MR1-6-FP or -5-OP-RU tetramer reactivity post-expansion as part of experiments shown in Fig. 7. (I and K) Percentages of IFNγ-producing expanded TRAV1-2+ or TRAV1-2− cells cultured in the absence or presence of MR1 deficient (C1R.MR1null), WT MR1 expressing (C1R.MR1null+MR1), or mutant (C1R.MR1null+MR1-K43A) expressing C1R cells pulsed with 10 nM 5-OP-RU, 10 μM 6-FP, or no antigen. Mean and SD are displayed. (J and L) Percentages of IFNγ-producing expanded TRAV1-2+ or TRAV1-2− cells cultured with WT or CD8-null MR1 expressing C1R cells pulsed with titrating doses of antigen. Data are from the same six (TRAV1-2+) or nine (TRAV1-2−) healthy blood donors as in Fig. 7, representing three independent experiments. Statistical significance was determined using a Friedman test with Dunn’s multiple comparison (I and K) or a two-way ANOVA with Sidak’s multiple comparisons test (J and L). (M) Top panels display dot plots of splenic T cells from a single donor stained directly ex vivo with WT or CD8-null MR1-5-OP-RU tetramers, gated on MAIT cells (elliptical gate) and other MR1-reactive T cells (polygon gate) and showing the frequency of total T cells. Bottom panels are dot plots of gated populations in top panels (Tetlow and Tethigh[MAIT]) displaying CD3 and TRAV1-2 expression. Data are from one experiment.
Figure 6.
Figure 6.
MR1-6-FP–reactive T cells are dependent on CD8 for MR1-6-FP tetramer recognition. (A) Expanded TRAV1-2− or TRAV1-2+ T cells stained with WT or CD8-null MR1-6-FP and MR1-5-OP-RU tetramers from a single healthy blood donor. (B) Comparison of WT and CD8-null MR1-6-FP and MR1-5-OP-RU tetramer staining of expanded TRAV1-2− cells from 12 donors. (C) Same format as B but of TRAV1-2+ T cells from six donors. (D) Comparison of WT and CD8-null MR1-5-OP-RU tetramer fluorescence of expanded TRAV1-2+ cells. Data are from three independent experiments. Statistical significance was determined using a two-way ANOVA with Sidak’s multiple comparisons test (B and C) or Wilcoxon signed-rank test (D).
Figure 7.
Figure 7.
MR1-6-FP T cell reactivity is reliant on CD8 for cytokine production. (A and C) Percentage of TNF-producing expanded TRAV1-2+ or TRAV1-2− cells cultured in the absence or presence of MR1 deficient (C1R.MR1null), WT MR1 expressing (C1R.MR1null+MR1), or mutant (C1R.MR1null+MR1-K43A) expressing C1R cells pulsed with 10 nM 5-OP-RU, 10 μM 6-FP, or no antigen. Mean and SD values are displayed. (B and D) Percentages of TNF-producing expanded TRAV1-2+ or TRAV1-2− cells cultured with WT or CD8-null MR1 expressing C1R cells pulsed with titrating doses of antigen. Data are from six (TRAV1-2+) or nine (TRAV1-2−) healthy blood donors from three independent experiments. Statistical significance was determined using a Friedman test with Dunn’s multiple comparison (A and C) or a two-way ANOVA with Sidak’s multiple comparisons test (B and D).
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