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Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks

Nature Immunology volume 13, pages 499–510 (2012)Cite this article

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Abstract

Lymph node stromal cells (LNSCs) closely regulate immunity and self-tolerance, yet key aspects of their biology remain poorly elucidated. Here, comparative transcriptomic analyses of mouse LNSC subsets demonstrated the expression of important immune mediators, growth factors and previously unknown structural components. Pairwise analyses of ligands and cognate receptors across hematopoietic and stromal subsets suggested a complex web of crosstalk. Fibroblastic reticular cells (FRCs) showed enrichment for higher expression of genes relevant to cytokine signaling, relative to their expression in skin and thymic fibroblasts. LNSCs from inflamed lymph nodes upregulated expression of genes encoding chemokines and molecules involved in the acute-phase response and the antigen-processing and antigen-presentation machinery. Poorly studied podoplanin (gp38)-negative CD31− LNSCs showed similarities to FRCs but lacked expression of interleukin 7 (IL-7) and were identified as myofibroblastic pericytes that expressed integrin α7. Together our data comprehensively describe the transcriptional characteristics of LNSC subsets.

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Figure 1: Strategy for sorting LNSCs and confirmation of microarray results.
Figure 2: Unbiased analysis of LNSCs provides insight into FRC function.
Figure 3: Expression of cytokines, growth factors and immunologically relevant receptors by stromal and hematopoietic cell subsets.
Figure 4: Transcriptional insights into the lymph-node conduit network.
Figure 5: Transcriptional specialization of FRCs, ThFs and SFs.
Figure 6: Cadherin-11 identifies junctions between lymph-node fibroblastic reticular cells.
Figure 7: DNCs are contractile pericytes.
Figure 8: LNSC response to inflammation.

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Acknowledgements

We thank L. Fisher (US National Institutes of Health) for polyclonal anti-decorin, anti-fibromodulin and anti-biglycan; M. Koch (University of Cologne) for polyclonal anti–collagen XIV; M. Curry for technical assistance in sorting stromal-cell populations; J.B. Lewis for discussions during analysis of microarray data; eBioscience, Affymetrix and Expression Analysis for support of the ImmGen Project; and K.W. Wucherpfennig for critical reading of the manuscript. Supported by the US National Institutes of Health (R01 DK074500 and P01 AI045757 to S.J.T.; R24 AI072073 to the ImmGen Consortium; R01 AI063428-06 to M.B.B.; R01 DE019917 to D.J.M.; and GM38903 to M.E.H. and K.K.), the Dana-Farber Cancer Institute (K.K. and V.L.-K.) and the Seventh Framework Programme of the European Union (Marie Curie International Outgoing Fellowship 220044 to S.F.G.).

Author information

Author notes

  1. Deepali Malhotra, Anne L Fletcher and Paul Monach: These authors contributed equally to this work.

  2. Adam J Best, Jamie Knell and Ananda Goldrath: Complete list of authors and affiliations appears at the end of this paper.

Authors and Affiliations

  1. Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Deepali Malhotra, Anne L Fletcher, Jillian Astarita, Veronika Lukacs-Kornek, Kutlu G Elpek, Konstantin Knoblich, Martin E Hemler & Shannon J Turley

  2. Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA

    Deepali Malhotra & Jillian Astarita

  3. School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA

    Prakriti Tayalia & David J Mooney

  4. Department of Pediatrics and Division of Rheumatology, Immunology, and Allergy, The Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA

    Santiago F Gonzalez & Michael C Carroll

  5. Brigham and Women's Hospital, Boston, Massachusetts, USA

    Sook Kyung Chang & Michael B Brenner

  6. Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA

    Michael B Brenner

  7. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA

    Shannon J Turley

  8. Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA

    Yan Zhou, Susan A Shinton & Richard R Hardy

  9. Department of Microbiology & Immunology, University of California San Francisco, San Francisco, California, USA

    Natalie A Bezman, Joseph C Sun, Charlie C Kim & Lewis L Lanier

  10. Icahn Medical Institute, Mount Sinai Hospital, New York, New York, USA

    Jennifer Miller, Brian Brown, Miriam Merad, Emmanuel L Gautier, Claudia Jakubzick & Gwendalyn J Randolph

  11. Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA

    Anne L Fletcher, Kutlu G Elpek, Angelique Bellemare-Pelletier, Deepali Malhotra, Shannon J Turley & Taras Kreslavsky

  12. Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA

    Deepali Malhotra

  13. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA

    Shannon J Turley, Tracy Heng, Michio Painter, Diane Mathis & Christophe Benoist

  14. University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Kavitha Narayan, Katelyn Sylvia & Joonsoo Kang

  15. Immune Disease Institute, Children's Hospital, Boston, Massachusetts, USA

    Roi Gazit, Brian Garrison & Derrick J Rossi

  16. Computer Science Department, Stanford University, Stanford, California, USA

    Vladimir Jojic & Daphne Koller

  17. Computer Science Department, Brown University, Providence, Rhode Island, USA

    Radu Jianu & David Laidlaw

  18. Department of Biomedical Engineering, Howard Hughes Medical Institute, Boston University, Boston, Massachusetts, USA

    James Costello & Jim Collins

  19. Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts, USA

    Nadia Cohen, Patrick Brennan & Michael B Brenner

  20. Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA

    Michael B Brenner

  21. Broad Institute, Cambridge, Massachusetts, USA

    Tal Shay & Aviv Regev

  22. Joslin Diabetes Center, Boston, Massachusetts, USA

    Francis Kim, Tata Nageswara Rao & Amy Wagers

  23. Department of Pathology & Immunology, Washington University, St. Louis, Missouri, USA

    Emmanuel L Gautier, Claudia Jakubzick & Gwendalyn J Randolph

  24. Department of Medicine, Boston University, Boston, Massachusetts, USA

    Paul Monach

  25. Division of Biological Sciences, University of California San Diego, La Jolla, California, USA

    Adam J Best, Jamie Knell & Ananda Goldrath

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  1. Deepali Malhotra
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  2. Anne L Fletcher
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Consortia

the Immunological Genome Project Consortium

  • Yan Zhou
  • , Susan A Shinton
  • , Richard R Hardy
  • , Natalie A Bezman
  • , Joseph C Sun
  • , Charlie C Kim
  • , Lewis L Lanier
  • , Jennifer Miller
  • , Brian Brown
  • , Miriam Merad
  • , Anne L Fletcher
  • , Kutlu G Elpek
  • , Angelique Bellemare-Pelletier
  • , Deepali Malhotra
  • , Shannon J Turley
  • , Kavitha Narayan
  • , Katelyn Sylvia
  • , Joonsoo Kang
  • , Roi Gazit
  • , Brian Garrison
  • , Derrick J Rossi
  • , Vladimir Jojic
  • , Daphne Koller
  • , Radu Jianu
  • , David Laidlaw
  • , James Costello
  • , Jim Collins
  • , Nadia Cohen
  • , Patrick Brennan
  • , Michael B Brenner
  • , Tal Shay
  • , Aviv Regev
  • , Francis Kim
  • , Tata Nageswara Rao
  • , Amy Wagers
  • , Emmanuel L Gautier
  • , Claudia Jakubzick
  • , Gwendalyn J Randolph
  • , Paul Monach
  • , Adam J Best
  • , Jamie Knell
  • , Ananda Goldrath
  • , Tracy Heng
  • , Taras Kreslavsky
  • , Michio Painter
  • , Diane Mathis
  •  & Christophe Benoist

Contributions

D.M. and A.L.F. designed the study, did and analyzed most experiments, and wrote the manuscript; S.J.T. designed and directed the study, analyzed and interpreted results, and wrote the manuscript; D.M. did primary analysis of the microarray data; V.L.-K., P.T., S.F.G., J.A., K.G.E. and K.K. did and analyzed individual experiments; and S.K.C., M.B.B., D.J.M., M.C.C. and M.E.H. contributed reagents and assisted with the analysis of individual experiments.

Corresponding author

Correspondence to Shannon J Turley.

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Competing interests

The authors declare no competing financial interests.

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Malhotra, D., Fletcher, A., Astarita, J. et al. Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks. Nat Immunol 13, 499–510 (2012). https://doi.org/10.1038/ni.2262

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