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:

Effector and stem-like memory cell fates are imprinted in distinct lymph node niches directed by CXCR3 ligands

Nature Immunology volume 22, pages 434–448 (2021)Cite this article

Subjects

Abstract

T cells dynamically interact with multiple, distinct cellular subsets to determine effector and memory differentiation. Here, we developed a platform to quantify cell location in three dimensions to determine the spatial requirements that direct T cell fate. After viral infection, we demonstrated that CD8+ effector T cell differentiation is associated with positioning at the lymph node periphery. This was instructed by CXCR3 signaling since, in its absence, T cells are confined to the lymph node center and alternatively differentiate into stem-like memory cell precursors. By mapping the cellular sources of CXCR3 ligands, we demonstrated that CXCL9 and CXCL10 are expressed by spatially distinct dendritic and stromal cell subsets. Unlike effector cells, retention of stem-like memory precursors in the paracortex is associated with CCR7 expression. Finally, we demonstrated that T cell location can be tuned, through deficiency in CXCL10 or type I interferon signaling, to promote effector or stem-like memory fates.

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: After LCMV infection, CD8+ T cells upregulate T-bet and migrate to the lymph node periphery to become short-lived Teff cells.
Fig. 2: Loss of CXCR3 promotes the formation of stem-like memory precursors.
Fig. 3: Diverging fates of WT and Cxcr3−/− P14 cells coincide with distinct lymph node locations.
Fig. 4: Conventional and inflammatory DCs express distinct profiles of CXCR3 ligands in spatially distinct lymph node niches.
Fig. 5: Stromal cell network produces distinct profiles of CXCL9 and CXCL10 after LCMV infection.
Fig. 6: Host deficiency in CXCL10 retains T cells in the lymph node paracortex and promotes formation of TSCM precursors.
Fig. 7: Retention of TSCM is associated with CCR7 expression.
Fig. 8: Host deficiency in type I IFN signaling tunes CD8+ T cell differentiation toward TSCM formation in the lymph node center.

Similar content being viewed by others

Data availability

The data that support the findings of this study are available from the corresponding authors upon reasonable request.

References

  1. Eickhoff, S. et al. Robust anti-viral immunity requires multiple distinct T cell-dendritic cell interactions. Cell 162, 1322–1337 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Groom, J. R. Regulators of T-cell fate: integration of cell migration, differentiation and function. Immunol. Rev. 289, 101–114 (2019).

    Article  CAS  PubMed  Google Scholar 

  3. Hor, J. L. et al. Spatiotemporally distinct interactions with dendritic cell subsets facilitates CD4+ and CD8+ T cell activation to localized viral infection. Immunity 43, 554–565 (2015).

    Article  CAS  PubMed  Google Scholar 

  4. Joshi, N. S. et al. Inflammation directs memory precursor and short-lived effector CD8+ T cell fates via the graded expression of T-bet transcription factor. Immunity 27, 281–295 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kaech, S. M. & Cui, W. Transcriptional control of effector and memory CD8+ T cell differentiation. Nat. Rev. Immunol. 12, 749–761 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Gautam, S. et al. The transcription factor c-Myb regulates CD8+ T cell stemness and antitumor immunity. Nat. Immunol. 20, 337–349 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Jeannet, G. et al. Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory. Proc. Natl Acad. Sci. USA 107, 9777–9782 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Zhou, X. et al. Differentiation and persistence of memory CD8+ T cells depend on T cell factor 1. Immunity 33, 229–240 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Gattinoni, L., Speiser, D. E., Lichterfeld, M. & Bonini, C. T memory stem cells in health and disease. Nat. Med. 23, 18–27 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Im, S. J. et al. Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature 537, 417–421 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Siddiqui, I. et al. Intratumoral Tcf1+PD-1+CD8+ T cells with stem-like properties promote tumor control in response to vaccination and checkpoint blockade immunotherapy. Immunity 50, 195–211.e10 (2019).

    Article  CAS  PubMed  Google Scholar 

  12. Raghu, D., Xue, H.-H. & Mielke, L. A. Control of lymphocyte fate, infection, and tumor immunity by TCF-1. Trends Immunol. 40, 1149–1162 (2019).

    Article  CAS  PubMed  Google Scholar 

  13. Jansen, C. S. et al. An intra-tumoral niche maintains and differentiates stem-like CD8 T cells. Nature 576, 465–470 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Blank, C. U. et al. Defining ‘T cell exhaustion’. Nat. Rev. Immunol. 19, 665–674 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Yao, C. et al. Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection. Nat. Immunol. 20, 890–901 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Guilliams, M. et al. Dendritic cells, monocytes and macrophages: a unified nomenclature based on ontogeny. Nat. Rev. Immunol. 14, 571–578 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Gerner, M. Y., Torabi-Parizi, P. & Germain, R. N. Strategically localized dendritic cells promote rapid T cell responses to lymph-borne particulate antigens. Immunity 42, 172–185 (2015).

    Article  CAS  PubMed  Google Scholar 

  18. Hickman, H. D. et al. Direct priming of antiviral CD8+ T cells in the peripheral interfollicular region of lymph nodes. Nat. Immunol. 9, 155–165 (2008).

    Article  CAS  PubMed  Google Scholar 

  19. De Simone, G et al. CXCR3 identifies human naive CD8+ T cells with enhanced effector differentiation potential. J. Immunol. 203, 3179–3189 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Hu, J. K., Kagari, T., Clingan, J. M. & Matloubian, M. Expression of chemokine receptor CXCR3 on T cells affects the balance between effector and memory CD8 T-cell generation. Proc. Natl Acad. Sci. USA 108, E118–E127 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  21. Kohlmeier, J. E. et al. Inflammatory chemokine receptors regulate CD8+ T cell contraction and memory generation following infection. J. Exp. Med. 208, 1621–1634 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Kurachi, M. et al. Chemokine receptor CXCR3 facilitates CD8+ T cell differentiation into short-lived effector cells leading to memory degeneration. J. Exp. Med. 208, 1605–1620 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Groom, J. R. & Luster, A. D. CXCR3 ligands: redundant, collaborative and antagonistic functions. Immunol. Cell Biol. 89, 207–215 (2011).

    Article  CAS  PubMed  Google Scholar 

  24. Groom, J. R. et al. CXCR3 chemokine receptor-ligand interactions in the lymph node optimize CD4+ T helper 1 cell differentiation. Immunity 37, 1091–1103 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Sung, J. H. et al. Chemokine guidance of central memory T cells is critical for antiviral recall responses in lymph nodes. Cell 150, 1249–1263 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kastenmuller, W., Torabi-Parizi, P., Subramanian, N., Lämmermann, T. & Germain, R. N. A spatially-organized multicellular innate immune response in lymph nodes limits systemic pathogen spread. Cell 150, 1235–1248 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Gregory, J. L. et al. Infection programs sustained lymphoid stromal cell responses and shapes lymph node remodeling upon secondary challenge. Cell Rep. 18, 406–418 (2017).

    Article  CAS  PubMed  Google Scholar 

  28. Rodda, L. B. et al. Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity. Immunity 48, 1014–1028.e6 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Alexandre, Y. O. & Mueller, S. N. Stromal cell networks coordinate immune response generation and maintenance. Immunol. Rev. 283, 77–85 (2018).

    Article  CAS  PubMed  Google Scholar 

  30. Brown, F. D. et al. Fibroblastic reticular cells enhance T cell metabolism and survival via epigenetic remodeling. Nat. Immunol. 20, 1668–1680 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Groom, J. R. Moving to the suburbs: T-cell positioning within lymph nodes during activation and memory. Immunol. Cell Biol. 93, 330–336 (2015).

    Article  CAS  PubMed  Google Scholar 

  32. Intlekofer, A. M. et al. Requirement for T-bet in the aberrant differentiation of unhelped memory CD8+ T cells. J. Exp. Med. 204, 2015–2021 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ollion, J., Cochennec, J., Loll, F., Escudé, C. & Boudier, T. TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. Bioinformatics 29, 1840–1841 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Ozga, A. J. et al. pMHC affinity controls duration of CD8+ T cell–DC interactions and imprints timing of effector differentiation versus expansion. J. Exp. Med. 213, 2811–2829 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Dose, M. et al. β-Catenin induces T-cell transformation by promoting genomic instability. Proc. Natl Acad. Sci. USA 111, 391–396 (2014).

    Article  CAS  PubMed  Google Scholar 

  36. Mielke, L. A. et al. TCF-1 limits the formation of Tc17 cells via repression of the MAF–RORγt axis. J. Exp. Med. 216, 1682–1699 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wu, T. et al. The TCF1-Bcl6 axis counteracts type I interferon to repress exhaustion and maintain T cell stemness. Sci. Immunol. 1, eaai8593 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Jadhav, R. R. et al. Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade. Proc. Natl Acad. Sci. USA 116, 14113–14118 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Danilo, M., Chennupati, V., Silva, J. G., Siegert, S. & Held, W. Suppression of Tcf1 by inflammatory cytokines facilitates effector CD8 T cell differentiation. Cell Rep. 22, 2107–2117 (2018).

    Article  CAS  PubMed  Google Scholar 

  40. Huang, Z. et al. IL-27 promotes the expansion of self-renewing CD8+ T cells in persistent viral infection. J. Exp. Med. 216, 1791–1808 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Marsman, C. et al. Plasmacytoid dendritic cell heterogeneity is defined by CXCL10 expression following TLR7 stimulation. Immunol. Cell Biol. 96, 1083–1094 (2018).

    Article  CAS  PubMed  Google Scholar 

  42. Chow, M. T. et al. Intratumoral activity of the CXCR3 chemokine system is required for the efficacy of anti-PD-1 therapy. Immunity 50, 1498–1512.e5 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Jung, Y. W., Rutishauser, R. L., Joshi, N. S., Haberman, A. M. & Kaech, S. M. Differential localization of effector and memory CD8 T cell subsets in lymphoid organs during acute viral infection. J. Immunol. 185, 5315–5325 (2010).

    Article  CAS  PubMed  Google Scholar 

  44. Dyer, D. Understanding the mechanisms that facilitate specificity, not redundancy, of chemokine-mediated leukocyte recruitment. Immunology 160, 336–344 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Metzemaekers, M., Vanheule, V., Janssens, R., Struyf, S. & Proost, P. Overview of the mechanisms that may contribute to the non-redundant activities of interferon-inducible CXC chemokine receptor 3 ligands. Front. Immunol. 8, 1970 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  46. DiToro, D. et al. Differential IL-2 expression defines developmental fates of follicular versus nonfollicular helper T cells. Science 361, eaao2933 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Sheikh, A. A. et al. Context-dependent role for T-bet in T follicular helper differentiation and germinal center function following viral infection. Cell Rep. 28, 1758–1772.e4 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Duckworth, B. C. & Groom, J. R. Conversations that count: cellular interactions that drive T cell fate. Immunol. Rev. https://doi.org/10.1111/imr.12945 (2021).

  49. Hancock, W. W. et al. Requirement of the chemokine receptor CXCR3 for acute allograft rejection. J. Exp. Med. 192, 1515–1520 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Pircher, H., Bürki, K., Lang, R., Hengartner, H. & Zinkernagel, R. M. Tolerance induction in double specific T-cell receptor transgenic mice varies with antigen. Nature 342, 559–561 (1989).

    Article  CAS  PubMed  Google Scholar 

  51. Park, M. K. et al. The CXC chemokine murine monokine induced by IFN-γ (CXC chemokine ligand 9) is made by APCs, targets lymphocytes including activated B cells, and supports antibody responses to a bacterial pathogen in vivo. J. Immunol. 169, 1433–1443 (2002).

    Article  CAS  PubMed  Google Scholar 

  52. Dufour, J. H. et al. IFN-γ-inducible protein 10 (IP-10; CXCL10)-deficient mice reveal a role for IP-10 in effector T cell generation and trafficking. J. Immunol. 168, 3195–3204 (2002).

    Article  CAS  PubMed  Google Scholar 

  53. Hwang, S. Y. et al. A null mutation in the gene encoding a type I interferon receptor component eliminates antiproliferative and antiviral responses to interferons alpha and beta and alters macrophage responses. Proc. Natl Acad. Sci. USA 92, 11284–11288 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Mombaerts, P. et al. RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68, 869–877 (1992).

    Article  CAS  PubMed  Google Scholar 

  55. Li, W., Germain, R. N. & Gerner, M. Y. Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D). Proc. Natl Acad. Sci. USA 114, E7321–E7330 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Preibisch, S. et al. Efficient Bayesian-based multiview deconvolution. Nat. Methods 11, 645–648 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Preibisch, S., Saalfeld, S., Schindelin, J. & Tomancak, P. Software for bead-based registration of selective plane illumination microscopy data. Nat. Methods 7, 418–419 (2010).

    Article  CAS  PubMed  Google Scholar 

  58. Ballester, M. et al. The nuclear localization of WAP and CSN genes is modified by lactogenic hormones in HC11 cells. J. Cell Biochem. 105, 262–270 (2008).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank S. L. Nutt, K. L. Good-Jacobson and K. D. Shortman for helpful discussions and/or critical reading of the manuscript. This work was supported by National Health and Medical Research Council (NHMRC) Ideas (no. GNT1182649) and Project (no. GNT1137989) grants to J.R.G.; grant nos. GNT1006592, GNT1045549 and GNT1065626 to M.P.; and grant no. GNT1185513 to L.A.M. B.C.D. is supported by a WEHI Academic Excellence scholarship. A.A.S. and L.D. are supported by Melbourne research scholarships. J.R.G. was supported by an Australian Research Council Future Fellowship (no. FT130100708) and is supported by a Walter and Eliza Hall Centenary Fellowship sponsored by CSL Behring. M.P. is supported by an NHMRC Investigator (no. GNT1175011) and Sylvia & Charles Viertel Senior Medical Research Fellowships. L.A.M. is supported by a Victorian Cancer Agency mid-career fellowship. The experimental scheme figures were generated with BioRender. This work was made possible through the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institutes Infrastructure Support Scheme.

Author information

Author notes

  1. Fanny Lafouresse

    Present address: Centre de Recherches en Cancérologie de Toulouse, INSERM U1037, Equipe Labellisée Ligue Nationale Contre le Cancer, Université de Toulouse III-Paul Sabatier, Toulouse, France

  2. Thomas Boudier

    Present address: Sorbonne Université, Paris, France

  3. These authors contributed equally: Brigette C. Duckworth, Fanny Lafouresse, Verena C. Wimmer.

Authors and Affiliations

  1. Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Brigette C. Duckworth, Fanny Lafouresse, Benjamin J. Broomfield, Lennard Dalit, Amania A. Sheikh, Raymond Z. Qin, Carolina Alvarado & Joanna R. Groom

  2. Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia

    Brigette C. Duckworth, Fanny Lafouresse, Verena C. Wimmer, Lennard Dalit, Amania A. Sheikh, Raymond Z. Qin, Marc Pellegrini, Thomas Boudier, Kelly L. Rogers & Joanna R. Groom

  3. Centre for Dynamic Imaging, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Verena C. Wimmer, Thomas Boudier & Kelly L. Rogers

  4. Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia

    Yannick O. Alexandre & Scott N. Mueller

  5. Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia

    Lisa A. Mielke

  6. Division of Infection and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia

    Marc Pellegrini

  7. The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, Victoria, Australia

    Scott N. Mueller

Authors
  1. Brigette C. Duckworth
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fanny Lafouresse
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Verena C. Wimmer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Benjamin J. Broomfield
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lennard Dalit
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yannick O. Alexandre
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Amania A. Sheikh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Raymond Z. Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Carolina Alvarado
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Lisa A. Mielke
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Marc Pellegrini
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Scott N. Mueller
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Thomas Boudier
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Kelly L. Rogers
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Joanna R. Groom
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.R.G. conceptualized the study. V.C.W., F.L., B.C.D., T.B., K.L.R. and S.N.M. devised the methodology. B.C.D., V.C.W., B.J.B., L.D., Y.O.A., C.A., A.A.S., R.Z.Q. and F.L. carried out the investigation. T.B., B.C.D., L.A.M. and F.L. carried out the software and formal analysis. V.C.W., B.C.D., F.L. and J.R.G. carried out the data vizualization. M.P. obtained the resources. J.R.G. and B.C.D. wrote the original draft and resubmission. J.R.G. acquired the funding and supervised the study.

Corresponding authors

Correspondence to Brigette C. Duckworth or Joanna R. Groom.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Immunology thanks the anonymous reviewers for their contribution to the peer review of this work. Zoltan Fehervari was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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

Extended data

Extended Data Fig. 1 Quantification of cells within 3D lymph nodes.

Cell position within lymph nodes were quantified using Eroded Volume Fraction analysis. (a,b) To determine the 3D structure, images were smoothed and global thresholding was set. (b) 3D distance map is computed inside the lymph nodes where EVF values are divided into 100 layers of equal volume from 0, near the lymph node periphery, to 1, the lymph node center. (c) To position cells within the lymph nodes cell images were top-hat filtered and cell signal threshold was set manually. (d) To determine the B cell follicle signal, images were smoothed and global thresholding was set. (e) Density of B220 B cell follicles (cyan), naïve (grey) and day 6 post LCMV infection (purple) P14 cells within intact lymph nodes. Lymph node periphery (EVF = 0) to lymph node center (EVF = 1). Data are pooled from 10 mice from 3 independent experiments. Data are mean ± SEM.

Extended Data Fig. 2 Uninfected P14 cell location and expression of ZsGreen_T-bet and CXCR3 during LCMV infection.

DsRED_ZsGreen_T-bet reporter P14 cells in LCMV infected WT hosts with control or αCD62L and FTY720 blocking treatments. (a) LSFM micrographs of uninfected inguinal lymph node, showing dsRED P14 (magenta) and ZsGreen_T-bet reporter (cyan) P14 cells. (b) Frequency and number of total P14 cells in lymph nodes in control or αCD62L/FTY720 treated mice at indicated days post LCMV infection. (c) Frequency and number of ZsTbet+CXCR3+ P14 cells in peripheral lymph nodes in control or αCD62L/FTY720 treated mice at indicated days post LCMV infection. (b,c) Data 3 mice per group and represent three independent experiments, total n = 10. Data are mean ± SEM.

Extended Data Fig. 3 Loss of CXCR3 promotes the formation of stem-like memory precursors.

GFP_WT or GFP_Cxcr3–/– P14 cells in LCMV infected WT hosts day 6 post infection (a,b) Representative histograms of (a) SLAMF6 and (b) SCA1 expression in naïve (CD44-CD8+) host, TSCM (CD44+TCF1+CD62L+) P14 or TSLEC (CD44+KLRG1+CD62L−) populations in WT and Cxcr3–/– P14 cells, gMFI for each population is shown. (c) Frequency of TSLEC (CD44+KLRG1+CD62L−) and (CD44+KLRG1+TCF1−), and TSCM (CD44+KLRG1−CD62L+), (CD44+KLRG1−TCF1+) and (CD44+TCF1+CD62L+) adoptively transferred GFP_WT or GFP_Cxcr3–/– P14 cells and WT polyclonal (GFP−CD44+CD8+) host T cells. Data are from 4 mice, and represent 3 independent experiments, total n = 10. Data are mean ± SEM. (d,f) Plots and (e,g) frequency of TSLEC (CD44+KLRG1+CD62L−) and TSCM (CD44+KLRG1−CD62L+) (d,e) GP33 and (f,g) NP396 tetramer+CD44+ cells in WT or Cxcr3–/– cells. p value indicates t-test between WT and Cxcr3–/– cells. (e,g) Data are from 5 mice, and represent 2 independent experiments, total n = 10. Data are mean ± SEM. (h) Plots and (i) time course of emergence of TSLEC (CD44+KLRG1+TCF1−) and TSCM (CD44+KLRG1−TCF1+) at indicated days post infection (h,i) Data are 4 mice per group and represent 3 independent experiments, total n = 10. Data are mean ± SEM.

Extended Data Fig. 4 Uninfected REX3 expression and DC gating strategy.

(a) LSFM micrographs of uninfected, REX3 inguinal lymph node, CXCL9-RFP (magenta), CXCL10-BFP (cyan), B220 (blue), CD31 (yellow). Lower panels show longitudinal slice through lymph node center. Data represent 6 independent replicates. (b) Gating strategy to define dendritic cell subsets. Digested lymph node cells were stained to identify CD11c+MHCII+ total DCs and subsets were defined within this gate, cDC1 (XCR1+CD11b+CD103+), cDC2 (Ly6C−SIRP1α+,CD11b+,CD103−) and moDC (CD64+Ly6C+SIRP1α+,CD11b+,CD103−).

Extended Data Fig. 5 Host deficiency in IFN-I signaling promotes stem-ness phenotype.

(a,d) Experimental schemes. GFP_P14 cells in WT or Ifnar–/– host mice were sorted day 6 post infection and transferred into naïve (a–c) Rag1–/– or (d-f) WT host mice, prior to infection with LCMV and harvest at either (a) day 14 post infection or (d) day 6 post infection (b,e) Plots and (c,f) total GFP_ P14 cells recovered from indicated hosts. Data are 3 and 4 mice per group and represent 2 independent experiments, total n = 8. Data are mean ± SEM.

Supplementary information

Reporting Summary

Supplementary Video 1

DsRED_ZsGreen_T-bet reporter P14 cells in LCMV-infected WT hosts. Cleared intact inguinal lymph node at day 6 p.i, showing dsRED P14 (magenta) ZsGreen_T-bet reporter (cyan) P14 cells.

Supplementary Video 2

DsRED_ZsGreen_T-bet reporter P14 cells in LCMV-infected WT hosts. LSFM 3D image of cleared intact inguinal lymph node at day 3 p.i, showing dsRED P14 (magenta) ZsGreen_T-bet reporter (cyan) P14 cells.

Supplementary Video 3

GFP_WT or GFP_Cxcr3–/– P14 cells in LCMV-infected WT hosts. Representative LSFM 3D images of cleared intact inguinal lymph nodes containing GFP_WT (left) or GFP_Cxcr3–/– (right) P14 cells at day 6 p.i, showing P14 cells (yellow), B220 (B cell follicles, cyan) and CD31 (lymphatic network, magenta).

Supplementary Video 4

GFP_WT or GFP_Cxcr3–/– P14 cells in LCMV-infected WT hosts with control or FTY720 treatment. LSFM 3D images of cleared intact inguinal lymph nodes containing GFP_WT (top left) or GFP_Cxcr3–/– (top right) FTY720-treated GFP_WT (lower left) or FTY720-treated GFP_Cxcr3–/– (lower right) P14 cells at day 6 p.i, showing P14 cells (yellow), B220 (B cell follicles, cyan) and CD31 (lymphatic network, magenta).

Supplementary Video 5

Intact REX3 reporter mice were infected with LCMV, and lymph nodes were analyzed at the indicated days post-infection. Representative LSFM 3D images of a cleared intact REX3 inguinal lymph node day 6 post-infection, showing CXCL9-RFP (magenta), CXCL10-BFP (cyan) and CD31 (lymphatic network, yellow).

Supplementary Video 6

REX3 bone-marrow-chimeric mice were infected with LCMV, and lymph nodes were analyzed at the indicated days post-infection. Representative LSFM 3D images of cleared REX3 BM chimeric inguinal lymph node day 6 post-infection, showing CXCL9-RFP (magenta), CXCL10-BFP (cyan) and CD31 (lymphatic network, yellow).

Supplementary Video 7

REX3 host chimeric mice were infected with LCMV, and lymph nodes were analyzed at the indicated days post-infection. Representative LSFM 3D images of cleared REX3 host chimeric inguinal lymph node day 6 post-infection, showing CXCL9-RFP (magenta), CXCL10-BFP (cyan) and CD31 (lymphatic network, yellow).

Supplementary Video 8

GFP_P14 cells in LCMV-infected WT and Ifnar–/– hosts. Representative LSFM 3D images of cleared intact popliteal lymph nodes containing WT (left) or Ifnar–/– (right) hosts at day 6 post-infection, showing P14 cells (yellow), B220 (B cell follicles, cyan) and CD31 (lymphatic network, magenta).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Duckworth, B.C., Lafouresse, F., Wimmer, V.C. et al. Effector and stem-like memory cell fates are imprinted in distinct lymph node niches directed by CXCR3 ligands. Nat Immunol 22, 434–448 (2021). https://doi.org/10.1038/s41590-021-00878-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41590-021-00878-5

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