Kyewski, B. & Klein, L. A central role for central tolerance. Annu. Rev. Immunol. 24, 571–606 (2006).
Nakagawa, Y. et al. Thymic nurse cells provide microenvironment for secondary T cell receptor-α rearrangement in cortical thymocytes. Proc. Natl Acad. Sci. USA 109, 20572–20577 (2012).
Klein, L., Hinterberger, M., Wirnsberger, G. & Kyewski, B. Antigen presentation in the thymus for positive selection and central tolerance induction. Nature Rev. Immunol. 9, 833–844 (2009).
Florea, B. I. et al. Activity-based profiling reveals reactivity of the murine thymoproteasome-specific subunit β5t. Chem. Biol. 17, 795–801 (2010).
Murata, S. et al. Regulation of CD8+ T cell development by thymus-specific proteasomes. Science 316, 1349–1353 (2007).
Nakagawa, T. et al. Cathepsin L: critical role in Ii degradation and CD4 T cell selection in the thymus. Science 280, 450–453 (1998).
Gommeaux, J. et al. Thymus-specific serine protease regulates positive selection of a subset of CD4+ thymocytes. Eur. J. Immunol. 39, 956–964 (2009).
Nedjic, J., Aichinger, M., Mizushima, N. & Klein, L. Macroautophagy, endogenous MHC II loading and T cell selection: the benefits of breaking the rules. Curr. Opin. Immunol. 21, 92–97 (2009).
Nedjic, J., Aichinger, M., Emmerich, J., Mizushima, N. & Klein, L. Autophagy in thymic epithelium shapes the T-cell repertoire and is essential for tolerance. Nature 455, 396–400 (2008).
Honey, K., Nakagawa, T., Peters, C. & Rudensky, A. Cathepsin L regulates CD4+ T cell selection independently of its effect on invariant chain: a role in the generation of positively selecting peptide ligands. J. Exp. Med. 195, 1349–1358 (2002).
Nitta, T. et al. Thymoproteasome shapes immunocompetent repertoire of CD8+ T cells. Immunity 32, 29–40 (2010).
Xing, Y., Jameson, S. C. & Hogquist, K. A. Thymoproteasome subunit-β5T generates peptide-MHC complexes specialized for positive selection. Proc. Natl Acad. Sci. USA 110, 6979–6984 (2013).
Ziegler, A., Muller, C. A., Bockmann, R. A. & Uchanska-Ziegler, B. Low-affinity peptides and T-cell selection. Trends Immunol. 30, 53–60 (2009).
Ryan, K. R., McNeil, L. K., Dao, C., Jensen, P. E. & Evavold, B. D. Modification of peptide interaction with MHC creates TCR partial agonists. Cell. Immunol. 227, 70–78 (2004).
Azzam, H. S. et al. CD5 expression is developmentally regulated by T cell receptor (TCR) signals and TCR avidity. J. Exp. Med. 188, 2301–2311 (1998).
Stefanova, I., Dorfman, J. R. & Germain, R. N. Self-recognition promotes the foreign antigen sensitivity of naive T lymphocytes. Nature 420, 429–434 (2002).
Cho, J. H., Kim, H. O., Surh, C. D. & Sprent, J. T cell receptor-dependent regulation of lipid rafts controls naive CD8+ T cell homeostasis. Immunity 32, 214–226 (2010).
Palmer, M. J., Mahajan, V. S., Chen, J., Irvine, D. J. & Lauffenburger, D. A. Signaling thresholds govern heterogeneity in IL-7-receptor-mediated responses of naive CD8+ T cells. Immunol. Cell Biol. 89, 581–594 (2011).
Mandl, J. N., Monteiro, J. P., Vrisekoop, N. & Germain, R. N. T cell-positive selection uses self-ligand binding strength to optimize repertoire recognition of foreign antigens. Immunity 38, 263–274 (2013).
References 18 and 19 show that T cell responsiveness is set in the thymus and maintained in mature T cells in proportion to the avidity of the positively selecting interaction. Reference 18 concludes that T cells with stronger affinity for self dominate in response to infections, whereas reference 19 challenges the generality of such correlations.
Persaud, S. P., Parker, C. R., Lo, W. L., Weber, K. S. & Allen, P. M. Intrinsic CD4+ T cell sensitivity and response to a pathogen are set and sustained by avidity for thymic and peripheral complexes of self peptide and MHC. Nature Immunol. 15, 266–274 (2014).
Surh, C. D. & Sprent, J. T-cell apoptosis detected in situ during positive and negative selection in the thymus. Nature 372, 100–103 (1994).
Daley, S. R., Hu, D. Y. & Goodnow, C. C. Helios marks strongly autoreactive CD4+ T cells in two major waves of thymic deletion distinguished by induction of PD-1 or NF-κB. J. Exp. Med. 210, 269–285 (2013).
Stritesky, G. L. et al. Murine thymic selection quantified using a unique method to capture deleted T cells. Proc. Natl Acad. Sci. USA 110, 4679–4684 (2013).
Using different approaches, references 22 and 23 quantify 'early' and 'late' negative selection in the cortex and the medulla, respectively, and conclude that the extent of clonal deletion in the cortex exceeds that in the medulla.
McCaughtry, T. M., Baldwin, T. A., Wilken, M. S. & Hogquist, K. A. Clonal deletion of thymocytes can occur in the cortex with no involvement of the medulla. J. Exp. Med. 205, 2575–2584 (2008).
Melichar, H. J., Ross, J. O., Herzmark, P., Hogquist, K. A. & Robey, E. A. Distinct temporal patterns of T cell receptor signaling during positive versus negative selection in situ. Sci. Signal. 6, ra92 (2013).
Irla, M., Hollander, G. & Reith, W. Control of central self-tolerance induction by autoreactive CD4+ thymocytes. Trends Immunol. 31, 71–79 (2010).
Mathis, D. & Benoist, C. Aire. Annu. Rev. Immunol. 27, 287–312 (2009).
Peterson, P., Org, T. & Rebane, A. Transcriptional regulation by AIRE: molecular mechanisms of central tolerance. Nature Rev. Immunol. 8, 948–957 (2008).
Gallegos, A. M. & Bevan, M. J. Central tolerance to tissue-specific antigens mediated by direct and indirect antigen presentation. J. Exp. Med. 200, 1039–1049 (2004).
Oukka, M., Cohen-Tannoudji, M., Tanaka, Y., Babinet, C. & Kosmatopoulos, K. Medullary thymic epithelial cells induce tolerance to intracellular proteins. J. Immunol. 156, 968–975 (1996).
Hinterberger, M. et al. Autonomous role of medullary thymic epithelial cells in central CD4+ T cell tolerance. Nature Immunol. 11, 512–519 (2010).
Through diminution of MHC class II on mTECs, this study documents an autonomous contribution of mTECs to both dominant and recessive mechanisms of CD4+ T cell tolerance and provides experimental support for the affinity model of TReg cell development versus clonal deletion.
Klein, L., Klein, T., Ruther, U. & Kyewski, B. CD4 T cell tolerance to human C-reactive protein, an inducible serum protein, is mediated by medullary thymic epithelium. J. Exp. Med. 188, 5–16 (1998).
Oukka, M. et al. CD4 T cell tolerance to nuclear proteins induced by medullary thymic epithelium. Immunity 4, 545–553 (1996).
Aschenbrenner, K. et al. Selection of Foxp3+ regulatory T cells specific for self antigen expressed and presented by Aire+ medullary thymic epithelial cells. Nature Immunol. 8, 351–358 (2007).
Atibalentja, D. F., Byersdorfer, C. A. & Unanue, E. R. Thymus-blood protein interactions are highly effective in negative selection and regulatory T cell induction. J. Immunol. 183, 7909–7918 (2009).
Klein, L., Roettinger, B. & Kyewski, B. Sampling of complementing self-antigen pools by thymic stromal cells maximizes the scope of central T cell tolerance. Eur. J. Immunol. 31, 2476–2486 (2001).
Munz, C. Enhancing immunity through autophagy. Annu. Rev. Immunol. 27, 423–449 (2009).
Aichinger, M., Wu, C., Nedjic, J. & Klein, L. Macroautophagy substrates are loaded onto MHC class II of medullary thymic epithelial cells for central tolerance. J. Exp. Med. 210, 287–300 (2013).
Mizushima, N. Autophagy in protein and organelle turnover. Cold Spring Harb. Symp. Quant. Biol. 76, 397–402 (2011).
Dongre, A. R. et al. In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses. Eur. J. Immunol. 31, 1485–1494 (2001).
Klein, L., Hinterberger, M., von Rohrscheidt, J. & Aichinger, M. Autonomous versus dendritic cell-dependent contributions of medullary thymic epithelial cells to central tolerance. Trends Immunol. 32, 188–193 (2011).
Koble, C. & Kyewski, B. The thymic medulla: a unique microenvironment for intercellular self-antigen transfer. J. Exp. Med. 206, 1505–1513 (2009).
Hubert, F. X. et al. Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance. Blood 118, 2462–2472 (2011).
Taniguchi, R. T. et al. Detection of an autoreactive T-cell population within the polyclonal repertoire that undergoes distinct autoimmune regulator (Aire)-mediated selection. Proc. Natl Acad. Sci. USA 109, 7847–7852 (2012).
Irla, M. et al. Autoantigen-specific interactions with CD4+ thymocytes control mature medullary thymic epithelial cell cellularity. Immunity 29, 451–463 (2008).
DeVoss, J. et al. Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. J. Exp. Med. 203, 2727–2735 (2006).
Fan, Y. et al. Thymus-specific deletion of insulin induces autoimmune diabetes. EMBO J. 28, 2812–2824 (2009).
Ehrlich, L. I., Oh, D. Y., Weissman, I. L. & Lewis, R. S. Differential contribution of chemotaxis and substrate restriction to segregation of immature and mature thymocytes. Immunity 31, 986–998 (2009).
Le Borgne, M. et al. The impact of negative selection on thymocyte migration in the medulla. Nature Immunol. 10, 823–830 (2009).
Ueda, Y. et al. Mst1 regulates integrin-dependent thymocyte trafficking and antigen recognition in the thymus. Nature Commun. 3, 1098 (2012).
Klein, L. Dead man walking: how thymocytes scan the medulla. Nature Immunol. 10, 809–811 (2009).
Derbinski, J., Pinto, S., Rosch, S., Hexel, K. & Kyewski, B. Promiscuous gene expression patterns in single medullary thymic epithelial cells argue for a stochastic mechanism. Proc. Natl Acad. Sci. USA 105, 657–662 (2008).
Pinto, S. et al. Overlapping gene coexpression patterns in human medullary thymic epithelial cells generate self-antigen diversity. Proc. Natl Acad. Sci. USA 110, E3497–3505 (2013).
Villasenor, J., Besse, W., Benoist, C. & Mathis, D. Ectopic expression of peripheral-tissue antigens in the thymic epithelium: probabilistic, monoallelic, misinitiated. Proc. Natl Acad. Sci. USA 105, 15854–15859 (2008).
Wu, L. & Shortman, K. Heterogeneity of thymic dendritic cells. Semin. Immunol. 17, 304–312 (2005).
Li, J., Park, J., Foss, D. & Goldschneider, I. Thymus-homing peripheral dendritic cells constitute two of the three major subsets of dendritic cells in the steady-state thymus. J. Exp. Med. 206, 607–622 (2009).
Joffre, O. P., Segura, E., Savina, A. & Amigorena, S. Cross-presentation by dendritic cells. Nature Rev. Immunol. 12, 557–569 (2012).
Proietto, A. I., Lahoud, M. H. & Wu, L. Distinct functional capacities of mouse thymic and splenic dendritic cell populations. Immunol. Cell Biol. 86, 700–708 (2008).
Lei, Y. et al. Aire-dependent production of XCL1 mediates medullary accumulation of thymic dendritic cells and contributes to regulatory T cell development. J. Exp. Med. 208, 383–394 (2011).
Baba, T., Nakamoto, Y. & Mukaida, N. Crucial contribution of thymic Sirpα+ conventional dendritic cells to central tolerance against blood-borne antigens in a CCR2-dependent manner. J. Immunol. 183, 3053–3063 (2009).
Atibalentja, D. F., Murphy, K. M. & Unanue, E. R. Functional redundancy between thymic CD8α+ and Sirpα+ conventional dendritic cells in presentation of blood-derived lysozyme by MHC class II proteins. J. Immunol. 186, 1421–1431 (2011).
Baba, T., Badr Mel, S., Tomaru, U., Ishizu, A. & Mukaida, N. Novel process of intrathymic tumor-immune tolerance through CCR2-mediated recruitment of Sirpα+ dendritic cells: a murine model. PLoS ONE 7, e41154 (2012).
Reizis, B., Colonna, M., Trinchieri, G., Barrat, F. & Gilliet, M. Plasmacytoid dendritic cells: one-trick ponies or workhorses of the immune system? Nature Rev. Immunol. 11, 558–565 (2011).
Villadangos, J. A. & Young, L. Antigen-presentation properties of plasmacytoid dendritic cells. Immunity 29, 352–361 (2008).
Wirnsberger, G., Mair, F. & Klein, L. Regulatory T cell differentiation of thymocytes does not require a dedicated antigen-presenting cell but is under T cell-intrinsic developmental control. Proc. Natl Acad. Sci. USA 106, 10278–10283 (2009).
Hadeiba, H. et al. Plasmacytoid dendritic cells transport peripheral antigens to the thymus to promote central tolerance. Immunity 36, 438–450 (2012).
This study shows that endogenous pDCs take up subcutaneously injected antigen and transport it to the thymus in a CCR9-dependent manner. Upon intravenous injection, antigen-loaded pDCs delete specific thymocytes, which indicates that migratory pDCs can support central tolerance.
Hadeiba, H. et al. CCR9 expression defines tolerogenic plasmacytoid dendritic cells able to suppress acute graft-versus-host disease. Nature Immunol. 9, 1253–1260 (2008).
Bonasio, R. et al. Clonal deletion of thymocytes by circulating dendritic cells homing to the thymus. Nature Immunol. 7, 1092–1100 (2006).
Akashi, K., Richie, L. I., Miyamoto, T., Carr, W. H. & Weissman, I. L. B lymphopoiesis in the thymus. J. Immunol. 164, 5221–5226 (2000).
Feyerabend, T. B. et al. Deletion of Notch1 converts pro-T cells to dendritic cells and promotes thymic B cells by cell-extrinsic and cell-intrinsic mechanisms. Immunity 30, 67–79 (2009).
Mori, S. et al. Presence of B cell progenitors in the thymus. J. Immunol. 158, 4193–4199 (1997).
Perera, J., Meng, L., Meng, F. & Huang, H. Autoreactive thymic B cells are efficient antigen-presenting cells of cognate self-antigens for T cell negative selection. Proc. Natl Acad. Sci. USA 110, 17011–17016 (2013).
Using BCR- and TCR-transgenic mice, this study shows that autoreactive thymic B cells are efficient APCs for negative selection. Thymic B cells may capture autoantigens through their BCR and present these to developing thymocytes for clonal deletion.
Frommer, F. & Waisman, A. B cells participate in thymic negative selection of murine auto-reactive CD4+ T cells. PLoS ONE 5, e15372 (2010).
Kleindienst, P., Chretien, I., Winkler, T. & Brocker, T. Functional comparison of thymic B cells and dendritic cells in vivo. Blood 95, 2610–2616 (2000).
Guerri, L. et al. Analysis of APC types involved in CD4 tolerance and regulatory T cell generation using reaggregated thymic organ cultures. J. Immunol. 190, 2102–2110 (2013).
Yuseff, M. I., Pierobon, P., Reversat, A. & Lennon-Dumenil, A. M. How B cells capture, process and present antigens: a crucial role for cell polarity. Nature Rev. Immunol. 13, 475–486 (2013).
Weiss, S. & Bogen, B. MHC class II-restricted presentation of intracellular antigen. Cell 64, 767–776 (1991).
Munthe, L. A., Corthay, A., Os, A., Zangani, M. & Bogen, B. Systemic autoimmune disease caused by autoreactive B cells that receive chronic help from Ig V region-specific T cells. J. Immunol. 175, 2391–2400 (2005).
Detanico, T., Heiser, R. A., Aviszus, K., Bonorino, C. & Wysocki, L. J. Self-tolerance checkpoints in CD4 T cells specific for a peptide derived from the B cell antigen receptor. J. Immunol. 187, 82–91 (2011).
Ebert, P. J., Jiang, S., Xie, J., Li, Q. J. & Davis, M. M. An endogenous positively selecting peptide enhances mature T cell responses and becomes an autoantigen in the absence of microRNA miR-181a. Nature Immunol. 10, 1162–1169 (2009).
Lo, W. L. et al. An endogenous peptide positively selects and augments the activation and survival of peripheral CD4+ T cells. Nature Immunol. 10, 1155–1161 (2009).
Martin, B. et al. Highly self-reactive naive CD4 T cells are prone to differentiate into regulatory T cells. Nature Commun. 4, 2209 (2013).
Hsieh, C. S., Lee, H. M. & Lio, C. W. Selection of regulatory T cells in the thymus. Nature Rev. Immunol. 12, 157–167 (2012).
Wirnsberger, G., Hinterberger, M. & Klein, L. Regulatory T-cell differentiation versus clonal deletion of autoreactive thymocytes. Immunol. Cell Biol. 89, 45–53 (2011).
Cowan, J. E. et al. The thymic medulla is required for Foxp3+ regulatory but not conventional CD4+ thymocyte development. J. Exp. Med. 210, 675–681 (2013).
Klein, L. & Jovanovic, K. Regulatory T cell lineage commitment in the thymus. Semin. Immunol. 23, 401–409 (2011).
Mathis, D. & Benoist, C. A decade of AIRE. Nature Rev. Immunol. 7, 645–650 (2007).
Malchow, S. et al. Aire-dependent thymic development of tumor-associated regulatory T cells. Science 339, 1219–1224 (2013).
This study reports that TReg cells that were consistently found to be enriched in prostate tumours of mice recognized an unknown antigen that was also present in the healthy prostate. These cells were found to differentiate as 'natural' (that is, thymically induced) TReg cells in an AIRE-dependent manner, which provides evidence for a link between AIRE-mediated expression of peripheral tissue antigens and the development of organ-specific TReg cells.
Bautista, J. L. et al. Intraclonal competition limits the fate determination of regulatory T cells in the thymus. Nature Immunol. 10, 610–617 (2009).
Leung, M. W., Shen, S. & Lafaille, J. J. TCR-dependent differentiation of thymic Foxp3+ cells is limited to small clonal sizes. J. Exp. Med. 206, 2121–2130 (2009).
Moran, A. E. et al. T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse. J. Exp. Med. 208, 1279–1289 (2011).
St-Pierre, C. et al. Transcriptome sequencing of neonatal thymic epithelial cells. Sci. Rep. 3, 1860 (2013).
Lv, H. et al. Impaired thymic tolerance to α-myosin directs autoimmunity to the heart in mice and humans. J. Clin. Invest. 121, 1561–1573 (2011).
Gottumukkala, R. V. et al. Myocardial infarction triggers chronic cardiac autoimmunity in type 1 diabetes. Sci. Transl Med. 4, 138ra180 (2012).
Gotter, J., Brors, B., Hergenhahn, M. & Kyewski, B. Medullary epithelial cells of the human thymus express a highly diverse selection of tissue-specific genes colocalized in chromosomal clusters. J. Exp. Med. 199, 155–166 (2004).
Durinovic-Bello, I. et al. Insulin gene VNTR genotype associates with frequency and phenotype of the autoimmune response to proinsulin. Genes Immun. 11, 188–193 (2010).
Pugliese, A. et al. The insulin gene is transcribed in the human thymus and transcription levels correlated with allelic variation at the INS VNTR-IDDM2 susceptibility locus for type 1 diabetes. Nature Genet. 15, 293–297 (1997).
Vafiadis, P. et al. Insulin expression in human thymus is modulated by INS VNTR alleles at the IDDM2 locus. Nature Genet. 15, 289–292 (1997).
Giraud, M. et al. An IRF8-binding promoter variant and AIRE control CHRNA1 promiscuous expression in thymus. Nature 448, 934–937 (2007).
Colobran, R. et al. Association of an SNP with intrathymic transcription of TSHR and Graves' disease: a role for defective thymic tolerance. Hum. Mol. Genet. 20, 3415–3423 (2011).
Klein, L., Klugmann, M., Nave, K. A., Tuohy, V. K. & Kyewski, B. Shaping of the autoreactive T-cell repertoire by a splice variant of self protein expressed in thymic epithelial cells. Nature Med. 6, 56–61 (2000).
de Jong, V. M. et al. Alternative splicing and differential expression of the islet autoantigen IGRP between pancreas and thymus contributes to immunogenicity of pancreatic islets but not diabetogenicity in humans. Diabetologia 56, 2651–2658 (2013).
Pinto, S. et al. Mis-initiation of intrathymic MART-1 transcription and biased TCR usage explain the high frequency of MART-1-specific T cells. Eur. J. Immunol. (in the press).
Scally, S. W. et al. A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis. J. Exp. Med. 210, 2569–2582 (2013).
van Lummel, M. et al. Post-translational modification of HLA-DQ binding islet-autoantigens in type 1 diabetes. Diabetes 63, 237–247 (2014).
Gascoigne, N. R. & Palmer, E. Signaling in thymic selection. Curr. Opin. Immunol. 23, 207–212 (2011).
Bains, I., van Santen, H. M., Seddon, B. & Yates, A. J. Models of self-peptide sampling by developing T cells identify candidate mechanisms of thymic selection. PLoS Comput. Biol. 9, e1003102 (2013).
Org, T. et al. The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep. 9, 370–376 (2008).
Koh, A. S. et al. Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity. Proc. Natl Acad. Sci. USA 105, 15878–15883 (2008).
Abramson, J., Giraud, M., Benoist, C. & Mathis, D. Aire's partners in the molecular control of immunological tolerance. Cell 140, 123–135 (2010).
Giraud, M. et al. Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells. Proc. Natl Acad. Sci. USA 109, 535–540 (2012).
Danso-Abeam, D., Humblet-Baron, S., Dooley, J. & Liston, A. Models of aire-dependent gene regulation for thymic negative selection. Frontiers Immunol. 2, 14 (2011).
Marrack, P., Ignatowicz, L., Kappler, J. W., Boymel, J. & Freed, J. H. Comparison of peptides bound to spleen and thymus class II. J. Exp. Med. 178, 2173–2183 (1993).
Collado, J. A. et al. Composition of the HLA-DR-associated human thymus peptidome. Eur. J. Immunol. 43, 2273–2282 (2013).
Espinosa, G. et al. Peptides presented by HLA class I molecules in the human thymus. J. Proteomics 94, 23–36 (2013).
Adamopoulou, E. et al. Exploring the MHC-peptide matrix of central tolerance in the human thymus. Nature Commun. 4, 2039 (2013).
Fortier, M. H. et al. The MHC class I peptide repertoire is molded by the transcriptome. J. Exp. Med. 205, 595–610 (2008).
Mester, G., Hoffmann, V. & Stevanovic, S. Insights into MHC class I antigen processing gained from large-scale analysis of class I ligands. Cell. Mol. Life Sci. 68, 1521–1532 (2011).
Millet, V., Naquet, P. & Guinamard, R. R. Intercellular MHC transfer between thymic epithelial and dendritic cells. Eur. J. Immunol. 38, 1257–1263 (2008).