Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids

Nature Immunology volume 19, pages 397–406 (2018)Cite this article

Abstract

The hallmark function of αβ T cell antigen receptors (TCRs) involves the highly specific co-recognition of a major histocompatibility complex molecule and its carried peptide. However, the molecular basis of the interactions of TCRs with the lipid antigen–presenting molecule CD1c is unknown. We identified frequent staining of human T cells with CD1c tetramers across numerous subjects. Whereas TCRs typically show high specificity for antigen, both tetramer binding and autoreactivity occurred with CD1c in complex with numerous, chemically diverse self lipids. Such extreme polyspecificity was attributable to binding of the TCR over the closed surface of CD1c, with the TCR covering the portal where lipids normally protrude. The TCR essentially failed to contact lipids because they were fully seated within CD1c. These data demonstrate the sequestration of lipids within CD1c as a mechanism of autoreactivity and point to small lipid size as a determinant of autoreactive T cell responses.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: CD1c tetramers stain human polyclonal T cells.
Fig. 2: Binding analysis of the 3C8 TCR by tetramer staining and surface plasmon resonance.
Fig. 3: Autoreactive T cell recognition of CD1a, CD1b and CD1c.
Fig. 4: Interaction between the 3C8 TCR and CD1c.
Fig. 5: Isolation of lipids from CD1c and 3C8 TCR–CD1c complexes.
Fig. 6: Models of the CD1c ligands in the X-ray crystal structures.
Fig. 7: CD1c-endo tetramer staining involves TCR binding and T cells with functional autoreactivity to CD1c proteins.
Fig. 8: CD1c monomers bind highly diverse self lipids, and tetramers derived therefrom bind to CD1c-autoreactive T cell clones.

Similar content being viewed by others

References

  1. Rossjohn, J. et al. T cell antigen receptor recognition of antigen-presenting molecules. Annu. Rev. Immunol. 33, 169–200 (2015).

    Article  CAS  PubMed  Google Scholar 

  2. Van Rhijn, I., Godfrey, D. I., Rossjohn, J. & Moody, D. B. Lipid and small-molecule display by CD1 and MR1. Nat. Rev. Immunol. 15, 643–654 (2015).

    Article  PubMed  Google Scholar 

  3. Adams, E. J. & Luoma, A. M. The adaptable major histocompatibility complex (MHC) fold: structure and function of nonclassical and MHC class I-like molecules. Annu. Rev. Immunol. 31, 529–561 (2013).

    Article  CAS  PubMed  Google Scholar 

  4. Godfrey, D. I., Uldrich, A. P., McCluskey, J., Rossjohn, J. & Moody, D. B. The burgeoning family of unconventional T cells. Nat. Immunol. 16, 1114–1123 (2015).

    Article  CAS  PubMed  Google Scholar 

  5. Gadola, S. D. et al. Structure of human CD1b with bound ligands at 2.3 A, a maze for alkyl chains. Nat. Immunol. 3, 721–726 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Zajonc, D. M. et al. Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor. Nat. Immunol. 6, 810–818 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Zajonc, D. M., Elsliger, M. A., Teyton, L. & Wilson, I. A. Crystal structure of CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A. Nat. Immunol. 4, 808–815 (2003).

    Article  CAS  PubMed  Google Scholar 

  8. Scharf, L. et al. The 2.5 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation. Immunity 33, 853–862 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Koch, M. et al. The crystal structure of human CD1d with and without alpha-galactosylceramide. Nat. Immunol. 6, 819–826 (2005).

    Article  CAS  PubMed  Google Scholar 

  10. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gras, S. et al. T cell receptor recognition of CD1b presenting a mycobacterial glycolipid. Nat. Commun. 7, 13257 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Shahine, A. et al. A molecular basis of human T cell receptor autoreactivity toward self-phospholipids. Sci. Immunol. 2, eaao1384 (2017).

  13. Birkinshaw, R. W. et al. αβ T cell antigen receptor recognition of CD1a presenting self lipid ligands. Nat. Immunol. 16, 258–266 (2015).

    Article  CAS  PubMed  Google Scholar 

  14. de Lalla, C. et al. High-frequency and adaptive-like dynamics of human CD1 self-reactive T cells. Eur. J. Immunol. 41, 602–610 (2011).

    Article  PubMed  Google Scholar 

  15. Roy, S. et al. Molecular analysis of lipid-reactive Vδ1 γδ T cells identified by CD1c tetramers. J. Immunol. 196, 1933–1942 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Roy, S. et al. Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells. Proc. Natl. Acad. Sci. USA 111, E4648–E4657 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Bagchi, S. et al. CD1b-autoreactive T cells contribute to hyperlipidemia-induced skin inflammation in mice. J. Clin. Invest. 127, 2339–2352 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Van Rhijn, I. et al. Human autoreactive T cells recognize CD1b and phospholipids. Proc. Natl. Acad. Sci. USA 113, 380–385 (2016).

    Article  CAS  PubMed  Google Scholar 

  19. Matulis, G. et al. Innate-like control of human iNKT cell autoreactivity via the hypervariable CDR3beta loop. PLoS Biol. 8, e1000402 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Mallevaey, T. et al. A molecular basis for NKT cell recognition of CD1d-self-antigen. Immunity 34, 315–326 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Gumperz, J. E. et al. Murine CD1d-restricted T cell recognition of cellular lipids. Immunity 12, 211–221 (2000).

    Article  CAS  PubMed  Google Scholar 

  22. de Jong, A. et al. CD1a-autoreactive T cells are a normal component of the human αβ T cell repertoire. Nat. Immunol. 11, 1102–1109 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  23. de Jong, A. et al. CD1a-autoreactive T cells recognize natural skin oils that function as headless antigens. Nat. Immunol. 15, 177–185 (2014).

    Article  PubMed  Google Scholar 

  24. Bourgeois, E. A. et al. Bee venom processes human skin lipids for presentation by CD1a. J. Exp. Med. 212, 149–163 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kim, J. H. et al. CD1a on Langerhans cells controls inflammatory skin disease. Nat. Immunol. 17, 1159–1166 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Subramaniam, S. et al. Elevated and cross-responsive CD1a-reactive T cells in bee and wasp venom allergic individuals. Eur. J. Immunol. 46, 242–252 (2016).

    Article  CAS  PubMed  Google Scholar 

  27. Mansour, S. et al. Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells. Proc. Natl. Acad. Sci. USA 113, E1266–E1275 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Lepore, M. et al. Targeting leukemia by CD1c-restricted T cells specific for a novel lipid antigen. OncoImmunology 4, e970463 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Yakimchuk, K. et al. Borrelia burgdorferi infection regulates CD1 expression in human cells and tissues via IL1-β. Eur. J. Immunol. 41, 694–705 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Roura-Mir, C. et al. CD1a and CD1c activate intrathyroidal T cells during Graves’ disease and Hashimoto’s thyroiditis. J. Immunol. 174, 3773–3780 (2005).

    Article  CAS  PubMed  Google Scholar 

  31. Lepore, M. et al. A novel self-lipid antigen targets human T cells against CD1c+ leukemias. J. Exp. Med. 211, 1363–1377 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ly, D. et al. CD1c tetramers detect ex vivo T cell responses to processed phosphomycoketide antigens. J. Exp. Med. 210, 729–741 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Altman, J. D. et al. Phenotypic analysis of antigen-specific T lymphocytes. Science 274, 94–96 (1996).

    Article  CAS  PubMed  Google Scholar 

  34. Guo, T. et al. A subset of human autoreactive CD1c-restricted T cells preferentially expresses TRBV4–1+ TCRs. J. Immunol. 200, 500–511 (2018).

    Article  CAS  PubMed  Google Scholar 

  35. Porcelli, S., Morita, C. T. & Brenner, M. B. CD1b restricts the response of human CD4–8– T lymphocytes to a microbial antigen. Nature 360, 593–597 (1992).

    Article  CAS  PubMed  Google Scholar 

  36. Yin, Y., Li, Y. & Mariuzza, R. A. Structural basis for self-recognition by autoimmune T-cell receptors. Immunol. Rev. 250, 32–48 (2012).

    Article  PubMed  Google Scholar 

  37. Melenhorst, J. J. et al. Contribution of TCR-β locus and HLA to the shape of the mature human Vβ repertoire. J. Immunol. 180, 6484–6489 (2008).

    Article  CAS  PubMed  Google Scholar 

  38. Dougan, S. K., Kaser, A. & Blumberg, R. S. CD1 expression on antigen-presenting cells. Curr. Top. Microbiol. Immunol. 314, 113–141 (2007).

    CAS  PubMed  Google Scholar 

  39. Vincent, M. S. et al. CD1-dependent dendritic cell instruction. Nat. Immunol. 3, 1163–1168 (2002).

    Article  CAS  PubMed  Google Scholar 

  40. Bligh, E. G. & Dyer, W. J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911–917 (1959).

    Article  CAS  PubMed  Google Scholar 

  41. Layre, E. et al. A comparative lipidomics platform for chemotaxonomic analysis of Mycobacterium tuberculosis. Chem. Biol. 18, 1537–1549 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Huang, S. et al. Discovery of deoxyceramides and diacylglycerols as CD1b scaffold lipids among diverse groove-blocking lipids of the human CD1 system. Proc. Natl Acad. Sci. USA 108, 19335–19340 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Madigan, C. A. et al. Lipidomic discovery of deoxysiderophores reveals a revised mycobactin biosynthesis pathway in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 109, 1257–1262 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Young, D. C. et al. In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection. Chem. Biol. 22, 516–526 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Gras, S. et al. Allelic polymorphism in the T cell receptor and its impact on immune responses. J. Exp. Med. 207, 1555–1567 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Wang, G. C., Dash, P., McCullers, J. A., Doherty, P. C. & Thomas, P. G. T cell receptor αβ diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection. Sci. Transl. Med. 4, 128ra42 (2012).

    PubMed  PubMed Central  Google Scholar 

  47. Holst, J., Vignali, K. M., Burton, A. R. & Vignali, D. A. A. Rapid analysis of T-cell selection in vivo using T cell-receptor retrogenic mice. Nat. Methods 3, 191–197 (2006).

    Article  CAS  PubMed  Google Scholar 

  48. Uldrich, A. P. et al. CD1d-lipid antigen recognition by the γδ TCR. Nat. Immunol. 14, 1137–1145 (2013).

    Article  CAS  PubMed  Google Scholar 

  49. 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).

    Article  PubMed  Google Scholar 

  50. Kjer-Nielsen, L. et al. A structural basis for the selection of dominant αβ T cell receptors in antiviral immunity. Immunity 18, 53–64 (2003).

    Article  CAS  PubMed  Google Scholar 

  51. Pellicci, D. G. et al. Differential recognition of CD1d-alpha-galactosyl ceramide by the Vβ8.2 and Vβ7 semi-invariant NKT T cell receptors. Immunity 31, 47–59 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Strong, M. et al. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103, 8060–8065 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. McCoy, A. J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D Biol. Crystallogr. 63, 32–41 (2007).

    Article  CAS  PubMed  Google Scholar 

  55. Bricogne, G. et al. autoBUSTER, Version 1.6.0. Global Phasing Ltd, Cambridge, United Kingdom. (2011).

  56. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank S. A. Porcelli (Albert Einstein College of Medicine, New York) for the 3C8 T cell clone; the Monash Macromolecular crystallization Facility staff for assistance with crystallization and the staff at the Australian synchrotron for assistance with data collection; D. Ly for advice on tetramer staining patterns; and L. L. Tan, H. Halim and N. Williams for technical assistance. Supported by the US National Institutes of Health (R01 AR048632, R01 AI049313 and AI U19111224), the Australian Research Council (Laureate Fellowship to J.R.), the National Health and Medical Research Council (Early Career Fellowship to K.S.W.) and the Wellcome Trust (Senior Investigator Award to D.A.P.).

Author information

Author notes

  1. These authors jointly supervised this work: D. Branch Moody and Jamie Rossjohn.

Authors and Affiliations

  1. Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia

    Kwok S. Wun, Jérôme Le Nours, Anthony W. Purcell, Stephanie Gras & Jamie Rossjohn

  2. ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia

    Kwok S. Wun, Jérôme Le Nours, Stephanie Gras & Jamie Rossjohn

  3. Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands

    Josephine F. Reijneveld & Ildiko Van Rhijn

  4. Brigham and Women’s Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA

    Josephine F. Reijneveld, Tan-Yun Cheng, Sara Suliman, Sarah Iwany, Jacob A. Mayfield, Ildiko Van Rhijn & D. Branch Moody

  5. Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK

    Kristin Ladell, Kelly L. Miners, James E. McLaren, Emma J. Grant, David A. Price & Jamie Rossjohn

  6. Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia

    Adam P. Uldrich & Dale I. Godfrey

  7. ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia

    Adam P. Uldrich & Dale I. Godfrey

  8. QIMR Berghofer Medical Research Institute, Herston, Australia

    Oscar L. Haigh

  9. Centre for Biodiscovery and Molecular Development of Therapeutics and Centre for Biosecurity and Tropical Infectious Diseases Australian Institute of Tropical Health and Medicine, James Cook University, Cairn, Australia

    Thomas S. Watkins & John J. Miles

  10. Socios en Salud Sucursal Peru, Lima, Peru

    Judith Jimenez, Roger Calderon, Kattya L. Tamara & Segundo R. Leon

  11. Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Megan B. Murray

  12. Emory University School of Medicine, Atlanta, GA, USA

    John D. Altman

Authors
  1. Kwok S. Wun
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Josephine F. Reijneveld
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tan-Yun Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kristin Ladell
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Adam P. Uldrich
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jérôme Le Nours
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kelly L. Miners
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. James E. McLaren
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Emma J. Grant
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Oscar L. Haigh
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Thomas S. Watkins
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Sara Suliman
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Sarah Iwany
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Judith Jimenez
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Roger Calderon
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Kattya L. Tamara
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Segundo R. Leon
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Megan B. Murray
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Jacob A. Mayfield
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. John D. Altman
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Anthony W. Purcell
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. John J. Miles
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Dale I. Godfrey
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Stephanie Gras
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. David A. Price
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Ildiko Van Rhijn
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. D. Branch Moody
    View author publications

    You can also search for this author in PubMed Google Scholar

  28. Jamie Rossjohn
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

K.S.W. undertook research, including the structural biology and surface plasmon resonance experiments, produced CD1c-lipid and TCR-CD1c-lipid complexes and analyzed data; J.F.R. produced CD1c-lipid complexes and isolated and analyzed T cell clones; T.-Y.C. eluted lipids for identification by MS; J.F.R., K.L., A.P.U., K.L.M., J.E.M., S.S., S.I., J.D.A., J.J.M. and I.V.R. generated tetramers or conducted tetramer staining experiments; K.L., J.J., S.R.L. and M.M. recruited and carried out clinical studies of healthy donors; J.L.N., E.J.G., O.L.H., T.S.W., R.C., K.L.T. and J.D.A. either provided key reagents or analyzed data; J.A.M. provided statistical analysis; K.L., A.W.P., D.I.G., S.G., D.A.P. and I.V.R. provided oversight for experiments and/or contributed to writing the paper; and D.B.M. and J.R. conceived of the project, provided oversight and wrote the paper.

Corresponding authors

Correspondence to D. Branch Moody or Jamie Rossjohn.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Integrated supplementary information

Supplementary Figure 1 Gating ancestry for tetramer stains in Fig. 1 and Supplementary Fig. 2.

(a) Gating ancestry for the CD1c-endo tetramer stains shown in Figure 1a (CD3+CD14–CD19–) and Supplemental Figure 2 (CD3–CD14–CD19–). (b) Gating ancestry for the CD1-endo and CD1b-endo tetramer stains and graphed data shown in Figure 1b and 1c.

Supplementary Figure 2 CD1c-endo tetramer binding to CD3– cells

CD1c-endo tetramer staining of live CD3–CD14–CD19– cells, pre-gated as shown in Supplementary Figure 1a. The corresponding CD1c-endo tetramer stains for CD3+CD14–CD19– cells are shown in Figure 1a.

Supplementary Figure 3 Sequence alignment of the different human CD1 isoforms

Residues on the CD1c α-helices that interacted with the 3C8 TCR are highlighted. Alanine-substituted residues are highlighted to indicate effects on CD69 expression by J76.3C8 cells: > 50% decrease, red; < 25% decrease, green. Residues that were not substituted are colored purple. * identical residue; : conserved residue;. conserved residue in 3 CD1 isoforms.

Supplementary Figure 4 Collision induced dissociation mass spectrometry of the CD1c ligand

Collision induced dissociation mass spectrometry of the CD1c ligand of m/z 359.316 is identified as monoacylglycerol (MAG) based on fragments corresponding to a single fatty acid (m/z 285.279) and a mass interval corresponding to glycerol. This pattern matches that derived from an authentic MAG standard.

Supplementary Figure 5 Reversed-phase analysis of lipids eluted from CD1c or 3C8 TCR–CD1c in HPLC-TOF-MS

Ions matching the expected retention time and m/z value of monoacylglycerol (MAG), sphingomyelin (SM), or phosphatidylcholine (PC) with a lipid moiety of CX:Y, where X is the total number of carbon atoms in the alkyl chain(s) and Y is the total number of unsaturations.

Supplementary Figure 6 Absolute quantification of lipids detected in association with CD1c or 3C8 TCR–CD1c using HPLC-TOF-MS

Lipids present in the eluents of the indicated CD1c or CD1c-TCR complex were compared to authentic standards of (a) MAG, (b) PC and (c) SM measured under the same conditions and expressed as area under the curve of the ion chromatogram (count-seconds). These values were used to calculate molar ratios of lipid ligands shown in Figure 5 (right). Data are representative of two independent experiments with similar results.

Supplementary Figure 7 Close up view of the CD1c antigen-binding pockets

(a) Superposition of CD1c-SL (cyan) onto the 3C8 TCR-CD1c-MAG (pink) structure showing the decanes and lauric acids occupying a position near the F′- and G′-portals 1. Despite occupying the same A′-pocket, the density modeled as MAG penetrated further into the antigen-binding cleft. (b) Electron density maps of MAG C16:0 and (c) stearic acid modeled into the 3C8 TCR-CD1c-endo crystal structure (blue, 2Fo-Fc = 1.0 σ), and (d) PC modeled into the CD1c-endo crystal structure (blue, 2Fo-Fc = 0.7 σ). (e) Close-up view of the interactions between residues in the CD1c binding pocket and MAG. (f) Spacer lipids in the F′-pocket housed within a network of hydrophobic residues. (g) Superposition of the previously solved CD1c-SL1, CD1c-MPM2 and CD1c-PM3 crystal structures onto the 3C8 TCR-CD1c-lipid and CD1c-lipid complexes. The CD1c molecule is displayed as gray surfaces, and residues that participated in forming the F′-roof are highlighted in violet. CD1c α-helices are colored as: CD1c-MAG, pink; CD1c-SL, cyan; CD1c-SM, green; CD1c-MPM, orange; and CD1c-PM, teal. MAG, pink sticks; Decane, purple sticks; Stearic acid, cyan sticks; PC, yellow sticks.

Supplementary Figure 8 Sorting of HD1CD4+ and HD1CD4– cells and treatment of MAG rescues staining with a SM-treated CD1c tetramer

(a) HD1CD4– cells and HD1CD4+ cells were stained with CD1c tetramer-APC or not, two weeks after sorting and stimulation with irradiated feeder cells and anti CD3 antibody. (b) CD1c monomers were first treated overnight with SM, or mock treated. Subsequently, ceramide, MAG, or diacylglycerol (DAG) was added and the CD1c-ligand mixtures were incubated overnight for a second time. The tetramerized monomers were used to stain the cell line HD1CD4+ (top), or HD1CD4– (bottom). Data are representative of 2 independent experiments with similar results.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wun, K.S., Reijneveld, J.F., Cheng, TY. et al. T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids. Nat Immunol 19, 397–406 (2018). https://doi.org/10.1038/s41590-018-0065-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41590-018-0065-7

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing