Medullary thymic epithelial cells (mTECs), which produce and present self-antigens, are essential for the establishment of central tolerance. Since mTEC numbers are limited, their function is complemented by thymic dendritic cells (DCs), which transfer mTEC-produced self-antigens via cooperative antigen transfer (CAT). While CAT is required for effective T cell selection, many aspects remain enigmatic. Given the recently described heterogeneity of mTECs and DCs, it is unclear whether the antigen acquisition from a particular TEC subset is mediated by preferential pairing with a specific subset of DCs. Using several relevant Cre-based mouse models that control for the expression of fluorescent proteins, we have found that, in regards to CAT, each subset of thymic DCs preferentially targets a distinct mTEC subset(s). Importantly, XCR1+-activated DC subset represented the most potent subset in CAT. Interestingly, thymic DCs can also acquire antigens from more than one mTEC, and of these, monocyte-derived dendritic cells (moDCs) were determined to be the most efficient. moDCs also represented the most potent DC subset in the acquisition of antigen from other DCs. These findings suggest a preferential pairing model for the distribution of mTEC-derived antigens among distinct populations of thymic DCs.

Department of Cell Biology Charles University Faculty of Science Charles University Prague Czech Republic

Division of Gastroenterology Hepatology and Endoscopy Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston United States

Laboratory of Immunobiology Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

Zobrazit více v PubMed

Adolph TE, Tomczak MF, Niederreiter L, Ko HJ, Böck J, Martinez-Naves E, Glickman JN, Tschurtschenthaler M, Hartwig J, Hosomi S, Flak MB, Cusick JL, Kohno K, Iwawaki T, Billmann-Born S, Raine T, Bharti R, Lucius R, Kweon MN, Marciniak SJ, Choi A, Hagen SJ, Schreiber S, Rosenstiel P, Kaser A, Blumberg RS. Paneth cells as a site of origin for intestinal inflammation. Nature. 2013;503:272–276. doi: 10.1038/nature12599. PubMed DOI PMC

Ardouin L, Luche H, Chelbi R, Carpentier S, Shawket A, Montanana Sanchis F, Santa Maria C, Grenot P, Alexandre Y, Grégoire C, Fries A, Vu Manh TP, Tamoutounour S, Crozat K, Tomasello E, Jorquera A, Fossum E, Bogen B, Azukizawa H, Bajenoff M, Henri S, Dalod M, Malissen B. Broad and Largely Concordant Molecular Changes Characterize Tolerogenic and Immunogenic Dendritic Cell Maturation in Thymus and Periphery. Immunity. 2016;45:305–318. doi: 10.1016/j.immuni.2016.07.019. PubMed DOI

Baba T, Nakamoto Y, Mukaida N. Crucial contribution of thymic Sirp alpha+ conventional dendritic cells to central tolerance against blood-borne antigens in a CCR2-dependent manner. Journal of Immunology. 2009;183:3053–3063. doi: 10.4049/jimmunol.0900438. PubMed DOI

Baran-Gale J, Morgan MD, Maio S, Dhalla F, Calvo-Asensio I, Deadman ME, Handel AE, Maynard A, Chen S, Green F, Sit RV, Neff NF, Darmanis S, Tan W, May AP, Marioni JC, Ponting CP, Holländer GA. Ageing compromises mouse thymus function and remodels epithelial cell differentiation. eLife. 2020;9:e56221. doi: 10.7554/eLife.56221. PubMed DOI PMC

Bautista JL, Cramer NT, Miller CN, Chavez J, Berrios DI, Byrnes LE, Germino J, Ntranos V, Sneddon JB, Burt TD, Gardner JM, Ye CJ, Anderson MS, Parent AV. Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla. Nature Communications. 2021;12:1096. doi: 10.1038/s41467-021-21346-6. PubMed DOI PMC

Boes M, Cerny J, Massol R, Op den Brouw M, Kirchhausen T, Chen J, Ploegh HL. T-cell engagement of dendritic cells rapidly rearranges MHC class II transport. Nature. 2002;418:983–988. doi: 10.1038/nature01004. PubMed DOI

Bornstein C, Nevo S, Giladi A, Kadouri N, Pouzolles M, Gerbe F, David E, Machado A, Chuprin A, Tóth B, Goldberg O, Itzkovitz S, Taylor N, Jay P, Zimmermann VS, Abramson J, Amit I. Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells. Nature. 2018;559:622–626. doi: 10.1038/s41586-018-0346-1. PubMed DOI

Breed ER, Watanabe M, Hogquist KA. Measuring Thymic Clonal Deletion at the Population Level. Journal of Immunology. 2019;202:3226–3233. doi: 10.4049/jimmunol.1900191. PubMed DOI PMC

Brennecke P, Reyes A, Pinto S, Rattay K, Nguyen M, Küchler R, Huber W, Kyewski B, Steinmetz LM. Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. Nature Immunology. 2015;16:933–941. doi: 10.1038/ni.3246. PubMed DOI PMC

Caton ML, Smith-Raska MR, Reizis B. Notch-RBP-J signaling controls the homeostasis of CD8- dendritic cells in the spleen. The Journal of Experimental Medicine. 2007;204:1653–1664. doi: 10.1084/jem.20062648. PubMed DOI PMC

Croxford AL, Lanzinger M, Hartmann FJ, Schreiner B, Mair F, Pelczar P, Clausen BE, Jung S, Greter M, Becher B. The Cytokine GM-CSF Drives the Inflammatory Signature of CCR2+ Monocytes and Licenses Autoimmunity. Immunity. 2015;43:502–514. doi: 10.1016/j.immuni.2015.08.010. PubMed DOI

Derbinski J, Schulte A, Kyewski B, Klein L. Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self. Nature Immunology. 2001;2:1032–1039. doi: 10.1038/ni723. PubMed DOI

Derbinski J, Pinto S, Rösch S, Hexel K, Kyewski B. Promiscuous gene expression patterns in single medullary thymic epithelial cells argue for a stochastic mechanism. PNAS. 2008;105:657–662. doi: 10.1073/pnas.0707486105. PubMed DOI PMC

Dhalla F, Baran-Gale J, Maio S, Chappell L, Holländer GA, Ponting CP. Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells. The EMBO Journal. 2020;39:e101828. doi: 10.15252/embj.2019101828. PubMed DOI PMC

Dobeš J, Neuwirth A, Dobešová M, Vobořil M, Balounová J, Ballek O, Lebl J, Meloni A, Krohn K, Kluger N, Ranki A, Filipp D. Gastrointestinal Autoimmunity Associated With Loss of Central Tolerance to Enteric α-Defensins. Gastroenterology. 2015;149:139–150. doi: 10.1053/j.gastro.2015.05.009. PubMed DOI

Gallegos AM, Bevan MJ. Central tolerance to tissue-specific antigens mediated by direct and indirect antigen presentation. The Journal of Experimental Medicine. 2004;200:1039–1049. doi: 10.1084/jem.20041457. PubMed DOI PMC

Gardner JM, Devoss JJ, Friedman RS, Wong DJ, Tan YX, Zhou X, Johannes KP, Su MA, Chang HY, Krummel MF, Anderson MS. Deletional tolerance mediated by extrathymic Aire-expressing cells. Science. 2008;321:843–847. doi: 10.1126/science.1159407. PubMed DOI PMC

Gordon J, Xiao S, Hughes B, Su D, Navarre SP, Condie BG, Manley NR. Specific expression of lacZ and cre recombinase in fetal thymic epithelial cells by multiplex gene targeting at the Foxn1 locus. BMC Developmental Biology. 2007;7:69. doi: 10.1186/1471-213X-7-69. PubMed DOI PMC

Guilliams M, Ginhoux F, Jakubzick C, Naik SH, Onai N, Schraml BU, Segura E, Tussiwand R, Yona S. Dendritic cells, monocytes and macrophages: a unified nomenclature based on ontogeny. Nature Reviews. Immunology. 2014;14:571–578. doi: 10.1038/nri3712. PubMed DOI PMC

Hu Z, Li Y, Van Nieuwenhuijze A, Selden HJ, Jarrett AM, Sorace AG, Yankeelov TE, Liston A, Ehrlich LIR. CCR7 Modulates the Generation of Thymic Regulatory T Cells by Altering the Composition of the Thymic Dendritic Cell Compartment. Cell Reports. 2017;21:168–180. doi: 10.1016/j.celrep.2017.09.016. PubMed DOI PMC

Janowska-Wieczorek A, Majka M, Kijowski J, Baj-Krzyworzeka M, Reca R, Turner AR, Ratajczak J, Emerson SG, Kowalska MA, Ratajczak MZ. Platelet-derived microparticles bind to hematopoietic stem/progenitor cells and enhance their engraftment. Blood. 2001;98:3143–3149. doi: 10.1182/blood.v98.10.3143. PubMed DOI

Kadouri N, Nevo S, Goldfarb Y, Abramson J. Thymic epithelial cell heterogeneity: TEC by TEC. Nature Reviews. Immunology. 2020;20:239–253. doi: 10.1038/s41577-019-0238-0. PubMed DOI

Klein L, Kyewski B, Allen PM, Hogquist KA. Positive and negative selection of the T cell repertoire: what thymocytes see (and don’t see) Nature Reviews. Immunology. 2014;14:377–391. doi: 10.1038/nri3667. PubMed DOI PMC

Klein L, Robey EA, Hsieh CS. Central CD4. Nature Reviews. Immunology. 2019;19:7–18. doi: 10.1038/s41577-018-0083-6. PubMed DOI

Koble C, Kyewski B. The thymic medulla: a unique microenvironment for intercellular self-antigen transfer. The Journal of Experimental Medicine. 2009;206:1505–1513. doi: 10.1084/jem.20082449. PubMed DOI PMC

Kroger CJ, Spidale NA, Wang B, Tisch R. Thymic Dendritic Cell Subsets Display Distinct Efficiencies and Mechanisms of Intercellular MHC Transfer. Journal of Immunology. 2017;198:249–256. doi: 10.4049/jimmunol.1601516. PubMed DOI PMC

Lancaster JN, Thyagarajan HM, Srinivasan J, Li Y, Hu Z, Ehrlich LIR. Live-cell imaging reveals the relative contributions of antigen-presenting cell subsets to thymic central tolerance. Nature Communications. 2019;10:2220. doi: 10.1038/s41467-019-09727-4. PubMed DOI PMC

Lei Y, Ripen AM, Ishimaru N, Ohigashi I, Nagasawa T, Jeker LT, Bösl MR, Holländer GA, Hayashi Y, Malefyt RDW, Nitta T, Takahama Y. Aire-dependent production of XCL1 mediates medullary accumulation of thymic dendritic cells and contributes to regulatory T cell development. The Journal of Experimental Medicine. 2011;208:383–394. doi: 10.1084/jem.20102327. PubMed DOI PMC

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. The Journal of Experimental Medicine. 2009;206:607–622. doi: 10.1084/jem.20082232. PubMed DOI PMC

Madisen L, Zwingman TA, Sunkin SM, Oh SW, Zariwala HA, Gu H, Ng LL, Palmiter RD, Hawrylycz MJ, Jones AR, Lein ES, Zeng H. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nature Neuroscience. 2010;13:133–140. doi: 10.1038/nn.2467. PubMed DOI PMC

Maier B, Leader AM, Chen ST, Tung N, Chang C, LeBerichel J, Chudnovskiy A, Maskey S, Walker L, Finnigan JP, Kirkling ME, Reizis B, Ghosh S, D’Amore NR, Bhardwaj N, Rothlin CV, Wolf A, Flores R, Marron T, Rahman AH, Kenigsberg E, Brown BD, Merad M. A conserved dendritic-cell regulatory program limits antitumour immunity. Nature. 2020;580:257–262. doi: 10.1038/s41586-020-2134-y. PubMed DOI PMC

Meredith M, Zemmour D, Mathis D, Benoist C. Aire controls gene expression in the thymic epithelium with ordered stochasticity. Nature Immunology. 2015;16:942–949. doi: 10.1038/ni.3247. PubMed DOI PMC

Metzger TC, Khan IS, Gardner JM, Mouchess ML, Johannes KP, Krawisz AK, Skrzypczynska KM, Anderson MS. Lineage tracing and cell ablation identify a post-Aire-expressing thymic epithelial cell population. Cell Reports. 2013;5:166–179. doi: 10.1016/j.celrep.2013.08.038. PubMed DOI PMC

Miller CN, Proekt I, von Moltke J, Wells KL, Rajpurkar AR, Wang H, Rattay K, Khan IS, Metzger TC, Pollack JL, Fries AC, Lwin WW, Wigton EJ, Parent AV, Kyewski B, Erle DJ, Hogquist KA, Steinmetz LM, Locksley RM, Anderson MS. Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development. Nature. 2018;559:627–631. doi: 10.1038/s41586-018-0345-2. PubMed DOI PMC

Mouri Y, Ueda Y, Yamano T, Matsumoto M, Tsuneyama K, Kinashi T, Matsumoto M. Mode of Tolerance Induction and Requirement for Aire Are Governed by the Cell Types That Express Self-Antigen and Those That Present Antigen. Journal of Immunology. 2017;199:3959–3971. doi: 10.4049/jimmunol.1700892. PubMed DOI

Oh J, Wu N, Barczak AJ, Barbeau R, Erle DJ, Shin JS. CD40 Mediates Maturation of Thymic Dendritic Cells Driven by Self-Reactive CD4 Thymocytes and Supports Development of Natural Regulatory T Cells. The Journal of Immunology. 2018;200:1399–1412. doi: 10.4049/jimmunol.1700768. PubMed DOI PMC

Park JE, Botting RA, Domínguez Conde C, Popescu DM, Lavaert M, Kunz DJ, Goh I, Stephenson E, Ragazzini R, Tuck E, Wilbrey-Clark A, Roberts K, Kedlian VR, Ferdinand JR, He X, Webb S, Maunder D, Vandamme N, Mahbubani KT, Polanski K, Mamanova L, Bolt L, Crossland D, de Rita F, Fuller A, Filby A, Reynolds G, Dixon D, Saeb-Parsy K, Lisgo S, Henderson D, Vento-Tormo R, Bayraktar OA, Barker RA, Meyer KB, Saeys Y, Bonfanti P, Behjati S, Clatworthy MR, Taghon T, Haniffa M, Teichmann SA. A cell atlas of human thymic development defines T cell repertoire formation. Science. 2020;367:6480. doi: 10.1126/science.aay3224. PubMed DOI PMC

Perry JSA, Lio CWJ, Kau AL, Nutsch K, Yang Z, Gordon JI, Murphy KM, Hsieh CS. Distinct Contributions of Aire and Antigen-Presenting-Cell Subsets to the Generation of Self-Tolerance in the Thymus. Immunity. 2014;41:414–426. doi: 10.1016/j.immuni.2014.08.007. PubMed DOI PMC

Perry JSA, Russler-Germain EV, Zhou YW, Purtha W, Cooper ML, Choi J, Schroeder MA, Salazar V, Egawa T, Lee BC, Abumrad NA, Kim BS, Anderson MS, DiPersio JF, Hsieh CS. Transfer of Cell-Surface Antigens by Scavenger Receptor CD36 Promotes Thymic Regulatory T Cell Receptor Repertoire Development and Allo-tolerance. Immunity. 2018;48:1271. doi: 10.1016/j.immuni.2018.05.011. PubMed DOI PMC

Sansom SN, Shikama-Dorn N, Zhanybekova S, Nusspaumer G, Macaulay IC, Deadman ME, Heger A, Ponting CP, Holländer GA. Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. Genome Research. 2014;24:1918–1931. doi: 10.1101/gr.171645.113. PubMed DOI PMC

Snippert HJ, van der Flier LG, Sato T, van Es JH, van den Born M, Kroon-Veenboer C, Barker N, Klein AM, van Rheenen J, Simons BD, Clevers H. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell. 2010;143:134–144. doi: 10.1016/j.cell.2010.09.016. PubMed DOI

Tykocinski LO, Sinemus A, Rezavandy E, Weiland Y, Baddeley D, Cremer C, Sonntag S, Willecke K, Derbinski J, Kyewski B. Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells. PNAS. 2010;107:19426–19431. doi: 10.1073/pnas.1009265107. PubMed DOI PMC

Venables T, Griffith AV, DeAraujo A, Petrie HT. Dynamic changes in epithelial cell morphology control thymic organ size during atrophy and regeneration. Nature Communications. 2019;10:4402. doi: 10.1038/s41467-019-11879-2. PubMed DOI PMC

Vobořil M, Brabec T, Dobeš J, Šplíchalová I, Březina J, Čepková A, Dobešová M, Aidarova A, Kubovčiak J, Tsyklauri O, Štěpánek O, Beneš V, Sedláček R, Klein L, Kolář M, Filipp D. Toll-like receptor signaling in thymic epithelium controls monocyte-derived dendritic cell recruitment and Treg generation. Nature Communications. 2020;11:2361. doi: 10.1038/s41467-020-16081-3. PubMed DOI PMC

Wang J, Sekai M, Matsui T, Fujii Y, Matsumoto M, Takeuchi O, Minato N, Hamazaki Y. Hassall’s corpuscles with cellular-senescence features maintain IFNα production through neutrophils and pDC activation in the thymus. International Immunology. 2019;31:127–139. doi: 10.1093/intimm/dxy073. PubMed DOI PMC

Wells KL, Miller CN, Gschwind AR, Wei W, Phipps JD, Anderson MS, Steinmetz LM. Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells. eLife. 2020;9:e60188. doi: 10.7554/eLife.60188. PubMed DOI PMC

Thymic mimetic cells function beyond self-tolerance

Mechanisms of Direct and Indirect Presentation of Self-Antigens in the Thymus