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Recirculating Foxp3+ regulatory T cells are restimulated in the thymus under Aire control

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Abstract

Thymically-derived Foxp3+ regulatory T cells (Treg) critically control immunological tolerance. These cells are generated in the medulla through high affinity interactions with medullary thymic epithelial cells (mTEC) expressing the Autoimmune regulator (Aire). Recent advances have revealed that thymic Treg contain not only developing but also recirculating cells from the periphery. Although Aire is implicated in the generation of Foxp3+ Treg, its role in the biology of recirculating Treg remains elusive. Here, we show that Aire regulates the suppressive signature of recirculating Treg independently of the remodeling of the medullary 3D organization throughout life where Treg reside. Accordingly, the adoptive transfer of peripheral Foxp3+ Treg in AireKO recipients led to an impaired suppressive signature upon their entry into the thymus. Furthermore, recirculating Treg from AireKO mice failed to attenuate the severity of multiorgan autoimmunity, demonstrating that their suppressive function is altered. Using bone marrow chimeras, we reveal that mTEC-specific expression of Aire controls the suppressive signature of recirculating Treg. Finally, mature mTEC lacking Aire were inefficient in stimulating peripheral Treg both in polyclonal and antigen-specific co-culture assays. Overall, this study demonstrates that Aire confers to mTEC the ability to restimulate recirculating Treg, unravelling a novel function for this master regulator in Treg biology.

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Data availability

All data generated or analyzed during this study are included in this published article and its supplementary information files. The dataset generated in this study are available in the Gene Expression Omnibus (GEO) database under accession number GSE188419.

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Acknowledgements

We are grateful to Georg Holländer (University of Basel, Switzerland) and Bernard Malissen (CIML, Marseille, France) for providing us AireKO and Foxp3eGFP mice, respectively. We thank the CIML flow cytometry, histology, PICSL imaging facility of the CIML (ImagImm) and animal facility platforms for technical support. We thank Cloé Zamit (CIML, France) for help with mouse genotyping.

Funding

This work was supported by institutional grants from INSERM, CNRS and Aix-Marseille Université.  The Immune Tolerance and T-Cell Differentiation laboratory received funding from the ARC Foundation (PJA20171206491 to M.I.), CoPoC-proof of concept (MAT-PI-17326-A-01 to M.I.), a prematuration grant from A*MIDEX, a French “Investissements d'avenir” program (LTalpha-Treg to M.I.) and Agence Nationale de la Recherche (grant ANR-19-CE18-0021–01, RANKLthym to M.I.). We also acknowledge financial support from France Bio Imaging (ANR-10-INBS-04–01) and France Génomique national infrastructure, funded as part of the "Investissements d'Avenir" program managed by the ANR (ANR-10-INBS-0009). J.C. and A.B. were supported by a PhD fellowship from the Ministère de l’Enseignement Supérieur et de la Recherche et de l’Innovation (MESRI).

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  1. Jonathan Charaix, Alexia Borelli have contributed equally to this work.

Authors and Affiliations

  1. Centre d’Immunologie de Marseille-Luminy, Aix-Marseille University, CNRS, INSERM, CIML, Marseille, France

    Jonathan Charaix, Alexia Borelli, Jérémy C. Santamaria, Lionel Chasson & Magali Irla

  2. Center for Research in Transplantation and Translational Immunology, UMR 1064, INSERM, Nantes Université, 44000, Nantes, France

    Matthieu Giraud

  3. Turing Centre for Living Systems, Laboratoire adhésion inflammation (LAI), CNRS, INSERM, Aix-Marseille University, 13288, Marseille, France

    Arnauld Sergé

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  1. Jonathan Charaix
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Contributions

JC, AB, JCS, LC and MI conducted the experiments, analyzed and interpreted the data. MG and AS analyzed the data. JC, AB, JCS and MI wrote the manuscript. MI initiated, supervised and conceived the study.

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Correspondence to Magali Irla.

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Movie S1. 3D rotation of AireWT thymic lobe of 9-day-old mouse, with medullary compartment colored according to their volume. AireWT thymic lobe (DAPI, blue) of a 9-day-old mouse is rendered in 3D with medullary compartments (Keratin 14, pseudo-colors) encoded according to medullary volumes from cyan (smallest medullae) to magenta (largest medullae). All axes are graduated with 500-µm grid spacing

Movie S2. 3D rotation of AireKO thymic lobe of 9-day-old mouse, with medullary compartment colored according to their volume. AireKO thymic lobe (DAPI, blue) of a 9-day-old mouse is rendered in 3D with medullary compartments (Keratin 14, pseudo-colors) encoded according to medullary volumes from cyan (smallest medullae) to magenta (largest medullae). All axes are graduated with 500-µm grid spacing

Movie S3. 3D rotation of AireWT thymic lobe of 6-week-old mouse, with medullary compartment colored according to their volume. AireWT thymic lobe (DAPI, blue) of a 6-week-old mouse is rendered in 3D with medullary compartments (Keratin 14, pseudo-colors) encoded according to medullary volumes from cyan (smallest medullae) to magenta (largest medullae). All axes are graduated with 500-µm grid spacing

Movie S4. 3D rotation of AireKO thymic lobe of 6-week-old mouse, with medullary compartment colored according to their volume. AireKO thymic lobe (DAPI, blue) of a 6-week-old mouse is rendered in 3D with medullary compartments (Keratin 14, pseudo-colors) encoded according to medullary volumes from cyan (smallest medullae) to magenta (largest medullae). All axes are graduated with 500-µm grid spacing

Movie S5. 3D rotation of AireWT thymic lobe of 1-year-old mouse, with medullary compartment colored according to their volume. AireWT thymic lobe (DAPI, blue) of a 1-year-old mouse is rendered in 3D with medullary compartments (Keratin 14, pseudo-colors) encoded according to medullary volumes from cyan (smallest medullae) to magenta (largest medullae). All axes are graduated with 500-µm grid spacing

Movie S6. 3D rotation of AireKO thymic lobe of 1-year-old mouse, with medullary compartment colored according to their volume. AireKO thymic lobe (DAPI, blue) of a 1-year-old mouse is rendered in 3D with medullary compartments (keratin 14, pseudo colors) encoded according to medullary volumes from cyan (smallest medullae) to magenta (largest medullae). All axes are graduated with 500-µm grid spacing

18_2022_4328_MOESM7_ESM.pdf

Fig. S1 Gating strategy used to purify recirculating CCR6+ Treg in the thymus. CD4+CD25+ cells were identified in CCR6+CD4+ T cells and analyzed for Foxp3 expression by flow cytometry.

Fig. S2 The suppressive signature of thymic CCR6+ Treg from 1-year-old AireKO mice is altered. The expression level of Foxp3, Klrg1, Il10, Gzmb, Fasl, Entpd1 and Nt5e was measured by qPCR in thymic CCR6+ Treg from 1-year-old AireWT (n=5-6) and AireKO (n=9) mice. Bar graphs show mean ± SEM, ns>0.05, ***p<0.001, ****p<0.0001 using two-tailed Mann–Whitney test.

Fig. S3 Splenic AireKO Treg show a normal suppressive signature throughout life. A, B Flow cytometry profiles, frequencies and numbers of CD4+Foxp3+ Treg in the blood of 6-week- (A) and 1-year-old (B) AireWT and AireKO mice. C, D Flow cytometry profiles, frequencies and numbers of CD4+Foxp3+ Treg in the spleen of 6-week- (C) and 1-year-old (D) AireWT or AireKO mice. Data are derived from 2 independent experiments (n=2-5 mice per group and per experiment). E, F The expression level of Foxp3, Il10, Tgfb1, Gzmb, Fasl, Lag3, Entpd1 and Nt5e was measured by qPCR in splenic Treg from 6-week- (E) and 1-year- (F) old AireWT (n=4-9 for 6 wk and n=8-13 for 1 yr) and AireKO (n=5-9 for 6 wk and n=8-13 for 1 yr) mice. Bar graphs show mean ± SEM, *p<0.05 and **p<0.01 using unpaired Student’s t test for C, D.

Fig. S4 The adoptive transfer of thymic CCR6+ Treg from AireKO mice fail to attenuate peripheral tissue infiltration. A Gating strategy used to sort CCR6+CD4+CD8-CD25+ cells, corresponding to CCR6+ Treg from the thymus of 6-week-old AireWT and AireKO mice. B Flow cytometry profiles and numbers of CD45.2 donor Treg in inguinal lymph nodes. C Flow cytometry profiles, frequencies and numbers of CD45.1 infiltrating cells in the pancreas, eyes and salivary glands. D Flow cytometry profiles and numbers of CD4+ and CD8+ T cells of CD45.1 origin infiltrating the pancreas, eyes and salivary glands. Data are derived from 3 independent experiments (n=2-5 mice per group and per experiment). Bar graphs show mean ± SEM, *p<0.05, **p<0.01, ***p<0.001 and ****p<0.0001 using two-tailed Mann–Whitney test for B or using unpaired Student’s t test for C,D.

Fig. S5 Aire expression in hematopoietic cells does not control the recirculation and suppressive signature of thymic CCR6+ Treg. A Experimental setup: Lethally irradiated CD45.1/2 WT recipients were reconstituted with CD45.2 AireWT or AireKO BM cells. Six weeks later, the recirculation and the suppressive signature of thymic CCR6+ Treg of CD45.2 origin were analyzed by flow cytometry and qPCR, respectively. B,C Flow cytometry profiles, frequencies and numbers of total B220+CD19+ B cells (B) and of IgD- or IgD+ cells in B220+CD19+ B cells (C). D,E Flow cytometry profiles, frequencies and numbers of CD25+ TregP, Foxp3lo TregP and CD25+Foxp3+ Treg (D) as well as CCR6- and CCR6+ cells in total CD25+Foxp3+ Treg (E). F The expression level of Foxp3, Klrg1, Il10, Gzmb, Fasl, Lag3, Entpd1 and Nt5e was measured by qPCR in CCR6+ Treg of CD45.2 origin purified from the thymus of AireWT (n=8) and AireKO (n=8) BM chimeric mice. Data are derived from 2 independent experiments (n=4 mice per group and per experiment). Bar graphs show mean ± SEM, *p<0.05 using two-tailed Mann–Whitney test for B, D.

Fig. S6 Gating strategy used to purify Aire+ mTEChi. Aire+ mTEChi were identified as EpCAM+Ly51-/loCD80+AireeGFP cells and purified from Airehet (AireeGFP/WT) and AireKO (AireeGFP/eGFP) mice. 

Fig. S7 AireKO mTEC express reduced levels of OX40L and GITRL. A Representative flow cytometry profiles of MHCII in mTEC from AireWT and AireKO mice. The histogram shows the frequency of MCHII+ mTEC. Bar graphs show mean ± SEM, **p<0.001 using two-tailed Mann–Whitney. B-C AireKO mTEC express reduced levels of OX40L and GITRL. Expression levels of Tnfsf4 (OX40L) and Tnfsf18 (GITRL) measured by RNA-seq (B) and flow cytometry (C) in AireWT and AireKO mTEChi. Bar graphs show mean ± SEM, **p<0.01 using two-tailed Mann–Whitney test for A.

Table S1. FPKM values of RNA-seq data derived from thymic CCR6+ Treg from AireWT and AireKO mice.

Table S2. List of antibodies used for flow cytometry.

Table S3. List of primers used for RT-qPCR.

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Charaix, J., Borelli, A., Santamaria, J.C. et al. Recirculating Foxp3+ regulatory T cells are restimulated in the thymus under Aire control. Cell. Mol. Life Sci. 79, 355 (2022). https://doi.org/10.1007/s00018-022-04328-9

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