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:

Membrane-anchored DNA nanojunctions enable closer antigen-presenting cell–T-cell contact in elevated T-cell receptor triggering

Nature Nanotechnology volume 18, pages 818–827 (2023)Cite this article

Subjects

An Author Correction to this article was published on 19 September 2023

This article has been updated

Abstract

How the engagement of a T-cell receptor to antigenic peptide-loaded major histocompatibility complex on antigen-presenting cells (APCs) initiates intracellular signalling cascades in T cells is not well understood. In particular, the dimension of the cellular contact zone is regarded as a determinant, but its influence remains controversial. This is due to the need for appropriate strategies for manipulating intermembrane spacing between the APC–T-cell interfaces without involving protein modification. Here we describe a membrane-anchored DNA nanojunction with distinct sizes to extend, maintain and shorten the APC–T-cell interface down to 10 nm. Our results suggest that the axial distance of the contact zone is critical in T-cell activation, presumably by modulating protein reorganization and mechanical force. Notably, we observe the promotion of T-cell signalling by shortening the intermembrane distance.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Fig. 1: Construction and characterization of TDNs for cell-surface engineering.
Fig. 2: Building DNJs for manipulation of intermembrane spacing.
Fig. 3: Influence of high-density DNJs on the activation of T cells.
Fig. 4: Modulating T-cell activation with DNJ-mediated intermembrane distance.
Fig. 5: Studying the molecular mechanism of TCR signalling.

Similar content being viewed by others

Data availability

The data supporting the findings of this study are available within the article and its Supplementary Information. Source data are provided with this paper and available via Zenodo at https://doi.org/10.5281/zenodo.7424802.

Code availability

The code designed for data collection and analysis of this study is available from the corresponding authors upon reasonable request.

Change history

References

  1. Weiss, A. & Dan, R. L. Signal transduction by lymphocyte antigen receptors. Cell 76, 263–274 (1994).

    Article  Google Scholar 

  2. Brownlie, R. J. & Zamoyska, R. T cell receptor signalling networks: branched, diversified and bounded. Nat. Rev. Immunol. 13, 257–269 (2013).

    Article  CAS  Google Scholar 

  3. Chakraborty, A. K. & Weiss, A. Insights into the initiation of TCR signaling. Nat. Immunol. 15, 798–807 (2014).

    Article  CAS  Google Scholar 

  4. Xu, X., Li, H. & Xu, C. Structural understanding of T cell receptor triggering. Cell. Mol. Immunol. 17, 193–202 (2020).

    Article  CAS  Google Scholar 

  5. Schamel, W. W., Alarcon, B. & Minguet, S. The TCR is an allosterically regulated macromolecular machinery changing its conformation while working. Immunol. Rev. 291, 8–25 (2019).

    Article  CAS  Google Scholar 

  6. Lee, M. S. et al. A mechanical switch couples T cell receptor triggering to the cytoplasmic juxtamembrane regions of CD3ζζ. Immunity 43, 227–239 (2015).

    Article  CAS  Google Scholar 

  7. Feng, Y., Reinherz, E. L. & Lang, M. J. αβ T cell receptor mechanosensing forces out serial engagement. Trends Immunol. 39, 596–609 (2018).

    Article  CAS  Google Scholar 

  8. Mckeithan, T. W. Kinetic proofreading in T-cell receptor signal transduction. Proc. Natl Acad. Sci. USA 92, 5042–5046 (1992).

    Article  Google Scholar 

  9. Rabinowitz, J. D., Beeson, C., Lyons, D. S. & Mcconnell, D. H. M. Kinetic discrimination in T-cell activation. Proc. Natl Acad. Sci. USA 93, 1401–1405 (1996).

    Article  CAS  Google Scholar 

  10. Huang, J. et al. The kinetics of two-dimensional TCR and pMHC interactions determine T-cell responsiveness. Nature 464, 932–936 (2010).

    Article  CAS  Google Scholar 

  11. Huppa, J. B. et al. TCR–peptide–MHC interactions in situ show accelerated kinetics and increased affinity. Nature 463, 963–967 (2010).

    Article  CAS  Google Scholar 

  12. Springer, T. A. Adhesion receptors of the immune system. Nature 346, 425–434 (1990).

    Article  CAS  Google Scholar 

  13. Choudhuri, K., Wiseman, D., Brown, M. H., Gould, K. G. & Der Merwe, P. A. V. T-cell receptor triggering is critically dependent on the dimensions of its peptide-MHC ligand. Nature 436, 578–582 (2005).

    Article  CAS  Google Scholar 

  14. Cai, H. et al. Full control of ligand positioning reveals spatial thresholds for T-cell receptor triggering. Nat. Nanotechnol. 13, 610–617 (2018).

    Article  CAS  Google Scholar 

  15. Sun, L. et al. DNA-edited ligand positioning on red blood cells to enable optimized T-cell activation for adoptive immunotherapy. Angew. Chem. Int. Ed. 59, 14842–14853 (2020).

    Article  CAS  Google Scholar 

  16. Garcia, K. C. et al. An alphabeta T-cell receptor structure at 2.5 Å and its orientation in the TCR–MHC complex. Science 274, 209–219 (1996).

    Article  CAS  Google Scholar 

  17. Birnbaum, M. E. et al. Deconstructing the peptide–MHC specificity of T-cell recognition. Cell 157, 1073–1087 (2014).

    Article  CAS  Google Scholar 

  18. McCall, M. N., Shotton, D. M. & Barclay, A. N. Expression of soluble isoforms of rat CD45. Analysis by electron microscopy and use in epitope mapping of anti-CD45R monoclonal antibodies. Immunology 76, 310–317 (1992).

    CAS  Google Scholar 

  19. Carbone, C. B. et al. In vitro reconstitution of T-cell receptor-mediated segregation of the CD45 phosphatase. Proc. Natl Acad. Sci. USA 114, E9338–E9345 (2017).

    Article  CAS  Google Scholar 

  20. Chang, V. T. et al. Initiation of T cell signaling by CD45 segregation at ‘close contacts’. Nat. Immunol. 17, 574–582 (2016).

    Article  CAS  Google Scholar 

  21. Hermiston, M. L., Xu, Z. & Weiss, A. CD45: a critical regulator of signaling thresholds in immune cells. Annu. Rev. Immunol. 21, 107–137 (2003).

    Article  CAS  Google Scholar 

  22. Davis, S. J. & van der Merwe, P. A. The kinetic-segregation model: TCR triggering and beyond. Nat. Immunol. 7, 803–809 (2006).

    Article  CAS  Google Scholar 

  23. Razvag, Y., Neve-Oz, Y., Sajman, J., Reches, M. & Sherman, E. Nanoscale kinetic segregation of TCR and CD45 in engaged microvilli facilitates early T cell activation. Nat. Commun. 9, 732 (2018).

    Article  Google Scholar 

  24. Li, Y.-C. et al. Cutting edge: mechanical forces acting on T cells immobilized via the TCR complex can trigger TCR signaling. J. Immunol. 184, 5959–5963 (2010).

    Article  CAS  Google Scholar 

  25. James, J. R. & Vale, R. D. Biophysical mechanism of T-cell receptor triggering in a reconstituted system. Nature 487, 64–69 (2012).

    Article  CAS  Google Scholar 

  26. Irles, C. et al. CD45 ectodomain controls interaction with GEMs and Lck activity for optimal TCR signaling. Nat. Immunol. 4, 189–197 (2003).

    Article  CAS  Google Scholar 

  27. Chen, B. et al. The affinity of elongated membrane-tethered ligands determines potency of T cell receptor triggering. Front. Immunol. 8, 793 (2017).

    Article  Google Scholar 

  28. Choudhuri, K. & van der Merwe, P. A. Molecular mechanisms involved in T cell receptor triggering. Semin. Immunol. 19, 255–261 (2007).

    Article  CAS  Google Scholar 

  29. van der Merwe, P. A. & Dushek, O. Mechanisms for T cell receptor triggering. Nat. Rev. Immunol. 11, 47–55 (2011).

    Article  Google Scholar 

  30. Malissen, B. & Bongrand, P. Early T cell activation: integrating biochemical, structural, and biophysical cues. Annu. Rev. Immunol. 33, 539–561 (2015).

    Article  CAS  Google Scholar 

  31. Courtney, A. H., Lo, W.-L. & Weiss, A. TCR signaling: mechanisms of initiation and propagation. Trends Biochem. Sci. 43, 108–123 (2018).

    Article  CAS  Google Scholar 

  32. Goodman, R. P. et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661–1665 (2005).

    Article  CAS  Google Scholar 

  33. Lin, M. et al. Programmable engineering of a biosensing interface with tetrahedral DNA nanostructures for ultrasensitive DNA detection. Angew. Chem. Int. Ed. 54, 2151–2155 (2015).

    Article  CAS  Google Scholar 

  34. Li, J. et al. Cell-membrane-anchored DNA nanoplatform for programming cellular interactions. J. Am. Chem. Soc. 141, 18013–18020 (2019).

    Article  CAS  Google Scholar 

  35. Jung, Y. et al. Three-dimensional localization of T-cell receptors in relation to microvilli using a combination of superresolution microscopies. Proc. Natl Acad. Sci. USA 113, E5916–E5924 (2016).

    Article  CAS  Google Scholar 

  36. Yi, J. C. & Samelson, L. E. Microvilli set the stage for T-cell activation. Proc. Natl Acad. Sci. USA 113, 11061–11062 (2016).

    Article  CAS  Google Scholar 

  37. Du, Y. et al. Ligand dilution analysis facilitates aptamer binding characterization at the single-molecule level. Angew. Chem. Int. Ed. 7, e202215387 (2022).

    Google Scholar 

  38. Huse, M. et al. Spatial and temporal dynamics of T cell receptor signaling with a photoactivatable agonist. Immunity 27, 76–88 (2007).

    Article  CAS  Google Scholar 

  39. Armstrong, J. K., Wenby, R. B., Meiselman, H. J. & Fisher, T. C. The hydrodynamic radii of macromolecules and their effect on red blood cell aggregation. Biophys. J. 87, 4259–4270 (2004).

    Article  CAS  Google Scholar 

  40. Zehn, D., Lee, S. Y. & Bevan, M. J. Complete but curtailed T-cell response to very low-affinity antigen. Nature 458, 211–214 (2009).

    Article  CAS  Google Scholar 

  41. Law, C. C. et al. Expression and characterization of recombinant soluble human CD3 molecules: presentation of antigenic epitopes defined on the native TCR–CD3 complex. Int. Immunol. 14, 389–400 (2002).

    Article  CAS  Google Scholar 

  42. Cohen, S. & Milstein, C. Structure of antibody molecules. Nature 214, 449–452 (1967).

    Article  CAS  Google Scholar 

  43. Mosayebi, M., Louis, A. A., Doye, J. P. K. & Ouldridge, T. E. Force-induced rupture of a DNA duplex: from fundamentals to force sensors. ACS Nano 9, 11993–12003 (2015).

    Article  CAS  Google Scholar 

  44. Furukawa, T., Itoh, M., Krueger, N. X., Streuli, M. & Saito, H. Specific interaction of the CD45 protein-tyrosine phosphatase with tyrosine-phosphorylated CD3 zeta chain. Proc. Natl Acad. Sci. USA 91, 10928–10932 (1994).

    Article  CAS  Google Scholar 

  45. Hegedus, Z. et al. Contribution of kinases and the CD45 phosphatase to the generation of tyrosine phosphorylation patterns in the T cell receptor complex ζ chain. Immunol. Lett. 67, 31–39 (1999).

    Article  CAS  Google Scholar 

  46. Straus, D. B. & Weiss, A. The CD3 chains of the T cell antigen receptor associate with the ZAP-70 tyrosine kinase and are tyrosine phosphorylated after receptor stimulation. J. Exp. Med. 178, 1523–1530 (1993).

    Article  CAS  Google Scholar 

  47. Chan, A. C., Iwashima, M., Turck, C. W. & Weiss, A. ZAP-70: a 70 kd protein-tyrosine kinase that associates with the TCR ζ chain. Cell 71, 649–662 (1992).

    Article  CAS  Google Scholar 

  48. Sherman, E. et al. Functional nanoscale organization of signaling molecules downstream of the T cell antigen receptor. Immunity 35, 705–720 (2011).

    Article  CAS  Google Scholar 

  49. Yokosuka, T. et al. Newly generated T cell receptor microclusters initiate and sustain T cell activation by recruitment of Zap70 and SLP-76. Nat. Immunol. 6, 1253–1262 (2005).

    Article  CAS  Google Scholar 

  50. Zhang, D. Y. & Seelig, G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103–113 (2011).

    Article  CAS  Google Scholar 

  51. Stone, J. D., Chervin, A. S. & Kranz, D. M. T cell receptor binding affinities and kinetics: impact on T cell activity and specificity. Immunology 126, 165–176 (2009).

    Article  CAS  Google Scholar 

  52. Valitutti, S., Müller, S., Cella, M., Padovan, E. & Lanzavecchia, A. Serial triggering of many T-cell receptors by a few peptide–MHC complexes. Nature 375, 148–151 (1995).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank X. Yu and Q. Zou at Shanghai Jiao Tong University School of Medicine for providing technical assistance. This work is supported by the National Key Research Program (2021YFA0910100 (to L.Q.), 2018YFC1602900 (to L.Q.) and 2019YFA0905800 (to W.T.)), the National Natural Science Foundation of China (NSFC 21922404 (to L.Q.), 22174039 (to L.Q.), 22107027 (to Y.L.) and 21827811 (to W.T.)), the Science and Technology Project of Hunan Province (2021RC4022 (to L.Q.), 2019SK2201 (to W.T.), 2018RS3035 (to L.Q.) and 2017XK2103 (to W.T.)) and Shenzhen excellent science and technology innovation talents training project (RCBS20200714114821377 (to Y.L.)).

Author information

Author notes

  1. These authors contributed equally: Yulin Du, Yifan Lyu.

Authors and Affiliations

  1. Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China

    Yulin Du, Yifan Lyu, Jie Lin, Chunran Ma, Qiang Zhang, Yutong Zhang, Liping Qiu & Weihong Tan

  2. The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China

    Liping Qiu & Weihong Tan

  3. Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China

    Weihong Tan

Authors
  1. Yulin Du
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yifan Lyu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jie Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chunran Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qiang Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yutong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Liping Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Weihong Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.D. and L.Q. conceived and designed the research. Y.D., Y.L., J.L., C.M., Q.Z. and Y.Z. conducted the experiments. Y.D. performed the analysis. Y.D. and Y.L. performed the imaging analysis and reconstruction of cell membrane morphology. Y.D., L.Q. and W.T. drafted and revised the manuscript. All the authors commented on the paper.

Corresponding authors

Correspondence to Liping Qiu or Weihong Tan.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Nanotechnology thanks Michael Dustin, Wolfgang Schamel and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

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

Supplementary information

Supplementary Information

Supplementary Figs. 1–44, Tables 1–4, unprocessed gels for Figs. 2, 15 and 35, Methods, and References.

Reporting Summary

Source data

Source Data Fig. 1

Statistical source data and unprocessed gels.

Source Data Fig. 2

Statistical source data.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Statistical source data.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Du, Y., Lyu, Y., Lin, J. et al. Membrane-anchored DNA nanojunctions enable closer antigen-presenting cell–T-cell contact in elevated T-cell receptor triggering. Nat. Nanotechnol. 18, 818–827 (2023). https://doi.org/10.1038/s41565-023-01333-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41565-023-01333-2

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