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A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+ Treg cell development


The neonatal thymus generates Foxp3+ regulatory T (tTreg) cells that are critical in controlling immune homeostasis and preventing multiorgan autoimmunity. The role of antigen specificity on neonatal tTreg cell selection is unresolved. Here we identify 17 self-peptides recognized by neonatal tTreg cells, and reveal ligand specificity patterns that include self-antigens presented in an age- and inflammation-dependent manner. Fate-mapping studies of neonatal peptidyl arginine deiminase type IV (Padi4)-specific thymocytes reveal disparate fate choices. Neonatal thymocytes expressing T cell receptors that engage IAb-Padi4 with moderate dwell times within a conventional docking orientation are exported as tTreg cells. In contrast, Padi4-specific T cell receptors with short dwell times are expressed on CD4+ T cells, while long dwell times induce negative selection. Temporally, Padi4-specific thymocytes are subject to a developmental stage-specific change in negative selection, which precludes tTreg cell development. Thus, a temporal switch in negative selection and ligand binding kinetics constrains the neonatal tTreg selection window.

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Fig. 1: TCRs expressed on neonate-derived tTreg cells can recognize steady-state antigens as well as inflammation- and age-dependent self-antigens.
Fig. 2: Identification of self-ligands recognized by neonatal tTreg TCRs using an immunopeptidome library screen.
Fig. 3: The development of Padi492–105-specific tTreg cells is restricted to the neonatal thymus.
Fig. 4: Padi4-specific tTreg cells seed the peripheral repertoire during the neonatal window and respond to inflammation.
Fig. 5: Padi4-specific thymocytes are subject to temporally regulated, stage-specific changes in negative selection.
Fig. 6: Limiting negative selection restores the development of Padi4-specific tTreg cells in the adult thymus.
Fig. 7: Padi4-specific neonatal tTreg cells express TCRs with modest dwell times.
Fig. 8: TCRs that promote neonatal negative selection, tTreg cell differentiation or CD4 Tconv cell development use conventional docking orientations on IAb-Padi4.

Data availability

TCR sequence data have been deposited in the NCBI Sequence Read Archive with accession code PRJNA534321. Coordinates and structure factors for the complexes 6235 TCR:IAb-Padi4, 4699 TCR:IAb-Padi4, 6256 TCR:IAb-Padi4, 5287 TCR:IAb-Padi4, 4378 TCR:IAb-Padi4 and 6236 TCR:IAb-Padi4 are available from the Protein Data Bank under accession codes 6MNO, 6MKD, 6MNM, 6MKR, 6MNG and 6MNN, respectively. All additional data that support the findings of this study are available from the corresponding author upon request.


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This work was supported by the US National Institutes of Health (DK095077, AR071269 and AI109858 to E.S.H.). X-ray diffraction data were collected at the LRL-CAT (31-ID) beamline at APS at the Argonne National Laboratory for PDB IDs 6MKD and 6MKR, and the FMX (17-ID-2) beamline at NSLS II at the Brookhaven National Laboratory for PDB IDs 6MNM, 6MNO, 6MNN and 6MNG.

Author information




B.D.S., S.J.B. and E.S.H. conceived and designed the project and interpreted the experiments. B.D.S. performed the TCR cloning and sequencing, flow cytometry and T cell activation experiments. B.D.S. and S.J.B. performed the structural, biophysical and statistical analyses. N.A.S., B.R.D. and P.G.H. performed the experiments. L.J.S. aided the mass spectrometry analyses. B.D.S., S.J.B. and E.S.H. wrote the manuscript.

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Correspondence to Eric S. Huseby.

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Supplementary Information

Supplementary Figs. 1–6 and Supplementary Tables 1–3.

Reporting Summary

Supplementary Dataset 1

IAb peptide library.

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Stadinski, B.D., Blevins, S.J., Spidale, N.A. et al. A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+ Treg cell development. Nat Immunol 20, 1046–1058 (2019).

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