Tolerance is established in polyclonal CD4+ T cells by distinct mechanisms, according to self-peptide expression patterns


Studies of repertoires of mouse monoclonal CD4+ T cells have revealed several mechanisms of self-tolerance; however, which mechanisms operate in normal repertoires is unclear. Here we studied polyclonal CD4+ T cells specific for green fluorescent protein expressed in various organs, which allowed us to determine the effects of specific expression patterns on the same epitope-specific T cells. Peptides presented uniformly by thymic antigen-presenting cells were tolerated by clonal deletion, whereas peptides excluded from the thymus were ignored. Peptides with limited thymic expression induced partial clonal deletion and impaired effector T cell potential but enhanced regulatory T cell potential. These mechanisms were also active for T cell populations specific for endogenously expressed self antigens. Thus, the immunotolerance of polyclonal CD4+ T cells was maintained by distinct mechanisms, according to self-peptide expression patterns.

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Figure 1: Three main patterns of tolerance to self antigens.
Figure 2: Ins1eGFP mice 'ignore' the eGFPp–I-Ab epitope.
Figure 3: eGFPp–I-Ab–specific CD4+ T cells undergo limited clonal deletion in the thymus.
Figure 4: High-affinity T cells are deleted in Ins2eGFP mice.
Figure 5: Aire-mediated thymic expression of eGFP promotes clonal deletion and Treg induction in Ins2eGFP mice.
Figure 6: Expression of a self epitope by thymic antigen-presenting cells induces intrathymic clonal deletion.
Figure 7: Frequency of self antigen–positive thymic antigen-presenting cells correlates with the responsiveness of the corresponding CD4+ T cell population.
Figure 8: Tolerance mechanisms identified in eGFP-expressing mouse strains govern tolerance to true self antigens.


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We thank D. Mueller for reviewing the manuscript; J. Walter and O. Rainwater for technical assistance; P. Lauer (and Aduro Biotech) for the Lm-eGFP strain PL1113. Supported by the US National Institutes of Health (P01 AI35296 to M.K.J. and K.A.H.; F32 AI114050 to D.M.; T32 GM008244 and F30 DK093242 to R.W.N.; T32 AI07313 to J.L.L.; K99 AI114884 to Y.J.L.), the Wallin Neuroscience Discovery Fund (to H.T.O. and M.K.J.) and the Juvenile Diabetes Research Foundation (2-2011-662 to B.T.F.).

Author information




D.M. designed the study, did experiments, analyzed data, and wrote the manuscript, J.L.L., T.D., Y.J.L., W.E.P., J.V.L., R.W.N. and M.S.A. did experiments, B.T.F., H.T.O. and K.A.H. provided discussions; and M.K.J. designed the study, analyzed data and wrote the manuscript.

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Correspondence to Marc K Jenkins.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Gating strategy for thymic epithelial cells and dendritic cells.

(a) Contour plots depicting the initial gating strategy for analysis of eGFP and eYFP expression by EpCAM+ thymic epithelial cells and dendritic cells. Briefly, thymuses were enzymatically digested to produce single cell suspensions, which were enriched for EpCAM+ and CD11c+ cells. Doublets were excluded. Numbers indicate the percent of cells in each gate.(b) Contour plots showing the gating strategy for EpCAM+ thymic epithelial cells, proceeding from singlet gate 2 (a). EpCAM+ CD45.2 stromal cells were gated for further analysis by excluding CD90.2+ T cells, dead cells, CD19+ B cells, macrophages and dendritic cells (CD11b+ and CD11c+). Remaining cells were analyzed further in Figure 7. Numbers indicate the percent of cells in the gate.(c) Contour plots showing the gating strategy for thymic dendritic cells, proceeding from singlet gate 2 (a). CD11c+ cells were gated and dead cells, CD90.2+ T cells, CD11chiCD11bhi eosinophils, CD19+ B cells, and autofluorescent macrophages (shaded, blue gate) were then excluded. Remaining CD11c+CD11blo–int cells were analyzed further in Figure 7. Numbers indicate the percent of cells carried forward for analysis.

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Malhotra, D., Linehan, J., Dileepan, T. et al. Tolerance is established in polyclonal CD4+ T cells by distinct mechanisms, according to self-peptide expression patterns. Nat Immunol 17, 187–195 (2016).

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