Central to adaptive immunity is the interaction between the αβ T cell receptor (TCR) and peptide presented by the major histocompatibility complex (MHC) molecule. Presumably reflecting TCR-MHC bias and T cell signaling constraints, the TCR universally adopts a canonical polarity atop the MHC. We report the structures of two TCRs, derived from human induced T regulatory (iTreg) cells, complexed to an MHC class II molecule presenting a proinsulin-derived peptide. The ternary complexes revealed a 180° polarity reversal compared to all other TCR-peptide-MHC complex structures. Namely, the iTreg TCR α-chain and β-chain are overlaid with the α-chain and β-chain of MHC class II, respectively. Nevertheless, this TCR interaction elicited a peptide-reactive, MHC-restricted T cell signal. Thus TCRs are not 'hardwired' to interact with MHC molecules in a stereotypic manner to elicit a T cell signal, a finding that fundamentally challenges our understanding of TCR recognition.
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Josefowicz, S.Z., Lu, L.-F. & Rudensky, A.Y. Regulatory T cells: mechanisms of differentiation and function. Annu. Rev. Immunol. 30, 531–564 (2012).
Rossjohn, J. et al. T cell antigen receptor recognition of antigen-presenting molecules. Annu. Rev. Immunol. 33, 169–200 (2015).
Gras, S. et al. A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol. Rev. 250, 61–81 (2012).
Garcia, K.C., Adams, J.J., Feng, D. & Ely, L.K. The molecular basis of TCR germline bias for MHC is surprisingly simple. Nat. Immunol. 10, 143–147 (2009).
Adams, J.J. et al. T Cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex. Immunity 35, 681–693 (2011).
Yin, L., Scott-Browne, J., Kappler, J.W., Gapin, L. & Marrack, P. T cells and their eons-old obsession with MHC. Immunol. Rev. 250, 49–60 (2012).
Feng, D., Bond, C.J., Ely, L.K., Maynard, J. & Garcia, K.C. Structural evidence for a germline-encoded T cell receptor–major histocompatibility complex interaction 'codon'. Nat. Immunol. 8, 975–983 (2007).
Garcia, K.C. Reconciling views on T cell receptor germline bias for MHC. Trends Immunol. 33, 429–436 (2012).
Dai, S. et al. Crossreactive T cells spotlight the germline rules for αβ T cell-receptor interactions with MHC molecules. Immunity 28, 324–334 (2008).
Scott-Browne, J.P. et al. Evolutionarily conserved features contribute to αβ T cell receptor specificity. Immunity 35, 526–535 (2011).
Weissler, K.A. & Caton, A.J. The role of T-cell receptor recognition of peptide: MHC complexes in the formation and activity of Foxp3+ regulatory T cells. Immunol. Rev. 259, 11–22 (2014).
Fuchs, E.J. Transplantation tolerance: from theory to clinic. Immunol. Rev. 258, 64–79 (2014).
Abbas, A.K. et al. Regulatory T cells: recommendations to simplify the nomenclature. Nat. Immunol. 14, 307–308 (2013).
Tree, T.I.M. et al. Naturally arising human CD4 T-cells that recognize islet autoantigens and secrete interleukin-10 regulate proinflammatory T-cell responses via linked suppression. Diabetes 59, 1451–1460 (2010).
Arif, S. et al. Autoreactive T cell responses show proinflammatory polarization in diabetes but a regulatory phenotype in health. J. Clin. Invest. 113, 451–463 (2004).
Roncarolo, M.-G. & Battaglia, M. Regulatory T-cell immunotherapy for tolerance to self antigens and alloantigens in humans. Nat. Rev. Immunol. 7, 585–598 (2007).
Kleijwegt, F.S. et al. Transfer of regulatory properties from tolerogenic to proinflammatory dendritic cells via induced autoreactive regulatory T cells. J. Immunol. 187, 6357–6364 (2011).
Ferreira Gabriela, B. et al. Vitamin D3 induces tolerance in human dendritic cells by activation of intracellular metabolic pathways. Cell Reports 10, 711–725 (2015).
Ferreira, G.B. et al. Differential protein pathways in 1,25-dihydroxyvitamin D3 and dexamethasone modulated tolerogenic human dendritic cells. J. Proteome Res. 11, 941–971 (2012).
Garcia, K.C. et al. An αβ T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex. Science 274, 209–219 (1996).
Deng, L. & Mariuzza, R.A. Recognition of self-peptide-MHC complexes by autoimmune T-cell receptors. Trends Biochem. Sci. 32, 500–508 (2007).
Bulek, A.M. et al. Structural basis for the killing of human beta cells by CD8+ T cells in type 1 diabetes. Nat. Immunol. 13, 283–289 (2012).
Yin, L. et al. A single T cell receptor bound to major histocompatibility complex class I and class II glycoproteins reveals switchable TCR conformers. Immunity 35, 23–33 (2011).
Reiser, J.B. et al. Crystal structure of a T cell receptor bound to an allogeneic MHC molecule. Nat. Immunol. 1, 291–297 (2000).
Stewart-Jones, G.B., McMichael, A.J., Bell, J.I., Stuart, D.I. & Jones, E.Y. A structural basis for immunodominant human T cell receptor recognition. Nat. Immunol. 4, 657–663 (2003).
Rossjohn, J., Pellicci, D.G., Patel, O., Gapin, L. & Godfrey, D.I. Recognition of CD1d-restricted antigens by natural killer T cells. Nat. Rev. Immunol. 12, 845–857 (2012).
Ding, Y.H. et al. Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids. Immunity 8, 403–411 (1998).
Gras, S. et al. A structural basis for varied αβ TCR usage against an immunodominant EBV antigen restricted to a HLA-B8 molecule. J. Immunol. 188, 311–321 (2012).
Broughton, S.E. et al. Biased T cell receptor usage directed against human leukocyte antigen DQ8-restricted gliadin peptides is associated with celiac disease. Immunity 37, 611–621 (2012).
Brownlie, R.J. & Zamoyska, R. T cell receptor signalling networks: branched, diversified and bounded. Nat. Rev. Immunol. 13, 257–269 (2013).
Hahn, M., Nicholson, M.J., Pyrdol, J. & Wucherpfennig, K.W. Unconventional topology of self peptide–major histocompatibility complex binding by a human autoimmune T cell receptor. Nat. Immunol. 6, 490–496 (2005).
Tynan, F.E. et al. T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I–bound peptide. Nat. Immunol. 6, 1114–1122 (2005).
Marrack, P., Scott-Browne, J.P., Dai, S., Gapin, L. & Kappler, J.W. Evolutionarily conserved amino acids that control TCR-MHC interaction. Annu. Rev. Immunol. 26, 171–203 (2008).
Van Laethem, F., Tikhonova, A.N. & Singer, A. MHC restriction is imposed on a diverse T cell receptor repertoire by CD4 and CD8 co-receptors during thymic selection. Trends Immunol. 33, 437–441 (2012).
Tikhonova, A.N. et al. αβ T cell receptors that do not undergo major histocompatibility complex-specific thymic selection possess antibody-like recognition specificities. Immunity 36, 79–91 (2012).
Shevach, E.M. & Thornton, A.M. tTregs, pTregs, and iTregs: similarities and differences. Immunol. Rev. 259, 88–102 (2014).
Vahl, J.C. et al. Continuous T cell receptor signals maintain a functional regulatory T cell pool. Immunity 41, 722–736 (2014).
Levine, A.G., Arvey, A., Jin, W. & Rudensky, A.Y. Continuous requirement for the TCR in regulatory T cell function. Nat. Immunol. 15, 1070–1078 (2014).
Birnbaum, M.E. et al. Molecular architecture of the αβ T cell receptor–CD3 complex. Proc. Natl. Acad. Sci. USA 111, 17576–17581 (2014).
Velthuis, J.H. et al. Accumulation of autoreactive effector T cells and allo-specific regulatory T cells in the pancreas allograft of a type 1 diabetic recipient. Diabetologia 52, 494–503 (2009).
Lamb, J.R., Eckels, D.D., Lake, P., Woody, J.N. & Green, N. Human T-cell clones recognize chemically synthesized peptides of influenza haemagglutinin. Nature 300, 66–69 (1982).
Gras, S. et al. Allelic polymorphism in the T cell receptor and its impact on immune responses. J. Exp. Med. 207, 1555–1567 (2010).
Aricescu, A.R., Lu, W. & Jones, E.Y. A time- and cost-efficient system for high-level protein production in mammalian cells. Acta Crystallogr. D Biol. Crystallogr. 62, 1243–1250 (2006).
Scally, S.W. et al. A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis. J. Exp. Med. 210, 2569–2582 (2013).
Van Rhijn, I. et al. A conserved human T cell population targets mycobacterial antigens presented by CD1b. Nat. Immunol. 14, 706–713 (2013).
We thank staff at the Australian synchrotron, the Leiden University Medical Center, the Monash Macromolecular Crystallization Facility, T. Beddoe, J. Teeler, C. van der Torren, S. Scally, M. Tran, S. Gras, K. Ladell, G. Dolton, R. Ayala-Perez and R. Berry for assistance. This work was supported by the Australian Research Council (ARC) and the National Health and Medical Research Council of Australia (NHMRC). A.P.U. is an ARC Future Fellow, D.I.G. is an NHMRC Senior Principal Research Fellow, D.A.P. is a Wellcome Trust Senior Investigator, K.J.R. is an NHMRC Career Development Fellow, A.W.P. is an NHMRC Senior Research Fellow, T.T. is an NHMRC Principal Research Fellow and J.R. is an NHMRC Australia Fellow. F.S.K., A.J. and B.O.R. are supported by the Netherlands Organization for Scientific Research (VICI 918.86.611), T.N. and S.L. are supported by the European Union 7th Framework Program (FP7/2007-2013) under Grant No. 241447 (Novel Immunotherapies for Type I Diabetes (NIAMIT)) and G.D. and A.R.v.d.S. are supported by the National Diabetes Expert Center funded by the Dutch Diabetes Research Foundation (DFN) and the Diabetes Research Netherlands (DON) Foundation.
The authors declare no competing financial interests.
Integrated supplementary information
Supplementary Figure 1 Phenotype and function of polyclonal T cell lines stimulated with autologous proinsulin C19-A3-loaded tDC (Treg) or inflammatory moDC (Teff).
(A) Expression of CD25, CD127, FoxP3, Granzyme B, IL-10 and IFNγ, associated with different subtypes of regulatory T cells, by Treg and Teff lines. (B) Treg-line but not Teff-line suppressed naive T cells proliferation (TnCFSE). Details of the suppression assay are described in the Methods section
(A) Mean fluorescence intensity expression of surface markers by iTreg clones (green) compared to effector T cell clones (red). Green circle shows a representative staining for iTreg clone FS18. Box and whiskers were generated according to Tukey. ***p<0.001, **p<0.01; 2-way ANOVA (for CD4, αβTCR, CD28 and GITR) and Mann-Whitney test (for CD62L). (B) Proliferation of clones derived from the Treg line upon stimulation with pro-insulin-loaded PBMC (black bars) or CMV-loaded PBMC (white bars). (C) IL-10 production by iTreg clones FS25 and FS17 upon stimulation with PBMC loaded with different concentrations of pro-insulin peptide.
An SA-omit map (a) was calculated using two round of simulated annealing in phenix.refine with a model without the peptide. The main features of the peptide are clearly visible in the SA-omit map. (b) After refinement in phenix.refine and buster the electron density of the peptide is well defined. Both maps were contoured at 1.2σ.
Electron density snapshots of FS18 TCR at a contour level of 1.2σ. The α-chain is in green and the β-chain in gray.
The FS17 HLA-DR4pro-insulin was superposed on the FS18 HLA-DR4pro-insulin by aligning the HLA-DRA domains in coot. FS18 is shown as a transparent cartoon. The TCR α chain is colored in lime green and the β chain in gray. The CDRs are colored as follows: CDR1α in red, CDR2α in pink, CDR3α in cyan, CDR1β in orange, CDR2β in purple, CDR3β in blue.
1x105 BLCL9031 APCs and either (a) 2x105 SKW3.SP3.4 or (b) 2x105 SKW3.FS18 T cells were incubated with or without the indicated amounts of a) DQ8-glia-α1 or b) C19-peptide in the presence or absence of 20μg/ml of blocking antibodies against HLA-DR4, HLA-DQ8, MHC-I and MHC-II for 16 hours at 37°C. Cells were harvested and stained with phycoerythrin-conjugated mouse anti-human CD3 (UCHT1; BD Pharmingen) and allophycocyanin-conjugated mouse anti-human CD69 (FN50; BD Pharmingen) and analyzed by flow cytometry. Representative CD3 versus CD69 plots of three independent experiments are shown.
1x105 BLCL9031 APCs and 2x105 SKW3.FS17 T cells were incubated without or with 50 μg/ml C19-(pro-insulin)-peptide in the presence or absence of 20 μg/ml of blocking antibodies against HLA-DR, HLA-DQ, MHC-I and MHC-II for 16 hours at 37°C. Cells were harvested and stained with V450-conjugated mouse anti-human CD3 (UCHT1; BD Pharmingen) and allophycocyanin-conjugated mouse anti-human CD69 (FN50; BD Pharmingen) and analyzed by flow cytometry.
2x105 BLCL9031 APCs were incubated with or without 50 μg/ml of (a) DQ8-glia-α1 or (b) hemagglutinin (HA)-peptide for 1 hour at 37°C. BLCL9031 cells were washed twice to remove excess amounts of peptide and antibody and incubated with 1x105 (a) SKW3.SP3.4 T cells or (b) SKW3.HA1.7 T cells. Cells were briefly spun down at 4°C to allow for cell-cell conjugation. T cells were the incubated with or without peptide-pulsed BLCL9031 APCs for the indicated times at 37°C. Un-stimulated cells were left on ice (untreated) in the presence of peptide-free BLCL9031 cells. Cells were fixed and permeabilized and stained with fluorochrome-conjugated antibodies for p-(Y418) SFK, p-(Y142) CD3ζ and p-(T202/Y204) ERK1/2 and analyzed by flow cytometry. Representative histograms of two independent experiments are shown.
1x105 SKW3.FS18 T cells, wt and mutants, were stained with V450-conjugated mouse anti-human CD3 (UCHT1; BD Pharmingen) and analyzed by flow cytometry. MFI of CD3-V450 was calculated in FlowJo and plotted in Prism (GraphPad Software). Quantified results are the means ± SD of four replicates and representative of three independent experiments.
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Beringer, D., Kleijwegt, F., Wiede, F. et al. T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex. Nat Immunol 16, 1153–1161 (2015) doi:10.1038/ni.3271
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