Thymoproteasome optimizes positive selection of CD8+ T cells without contribution of negative selection

Abstract

Functionally competent and self-tolerant T cell repertoire is shaped through positive and negative selection in the cortical and medullary microenvironments of the thymus. The thymoproteasome specifically expressed in the cortical thymic epithelium is essential for the optimal generation of CD8⁺ T cells. Although how the thymoproteasome governs the generation of CD8⁺ T cells is not fully understood, accumulating evidence suggests that the thymoproteasome optimizes CD8⁺ T cell production through the processing of self-peptides associated with MHC class I molecules expressed by cortical thymic epithelial cells. In this review, we describe recent advances in the mechanism of thymoproteasome-dependent generation of CD8⁺ T cells, focusing on the process of cortical positive selection independent of apoptosis-mediated negative selection.

Keywords: Negative selection; Positive selection; T cell repertoire; T cell selection; Thymic cortex; Thymic medulla; Thymoproteasome; Thymus; β5t.

Fig. 1

Trans-omics analysis of TECs. Correlation plot analysis of trans-omic (proteomic and transcriptomic) profiles for (A) β5t-deficient cTECs and wildtype (WT) cTECs and (B) WT cTECs and WT mTECs. (A) Among 91 molecules (blue symbols) that were more highly detected (P<0.05) in β5t-deficient cTECs than in WT cTECs in both proteomic and transcriptomic data, none of the molecules showed the fold changes in proteomic data >0.5 and transcriptomic data >2 (indicated by green dot lines). Among 121 molecules (red symbols) that were more highly detected (P<0.05) in WT cTECs than in β5t-deficient cTECs in both proteomic and transcriptomic data, 2 molecules showed the fold changes in proteomic data <−0.5 and transcriptomic data <−2. Among these 2 molecules, only one molecule β5t showed a reproducible reduction in β5t-deficient cTECs in individual quantitative analysis. (B) In the parallel analysis using the same threshold setting, among 479 molecules (blue symbols) that were more highly detected in cTECs than in mTECs, 66 molecules showed the fold changes in proteomic data >0.5 and transcriptomic data >2 (indicated by green dot lines). Among 539 molecules (red symbols) that were more highly detected in mTECs than in cTECs, 213 molecules showed the fold changes in proteomic data <−0.5 and transcriptomic data <−2.

Fig. 2

Thymoproteasome and thymic selection. (A) Thymic selection in normal thymus. cTEC-specific thymoproteasome produces a unique set of MHC-I-associated peptides (red symbols) that induce positive selection in the thymic cortex. Positively selected thymocytes (red cells) are screened for negative selection in the cortex and medulla, and a fraction of thymocytes are negatively selected to establish self-tolerance. (B) According to the peptide switch hypothesis, positive selection-inducing MHC-associated peptides must be different from negative selection-inducing MHC-associated peptides. In the conditions that lack the machinery to produce a unique set of MHC-I-associated peptides, a set of MHC-I-associated peptides identical to negative selection-inducing peptides (yellow symbols) are displayed by cTECs and positively select a repertoire of thymocytes in the thymic cortex; however, these thymocytes are subsequently negatively selected in the thymus by the interaction with identical set of MHC-I-associated peptides. Thus, the lack of the peptide switch may not reduce the number of positively selected thymocytes in the cortex (yellow cells) but may enhance the number of negatively selected thymocytes. (C) However, it was shown that in the thymus of β5t-knockout (KO) mice, the number of positively selected thymocytes in the cortex are reduced (green cells), whereas the number of negatively selected thymocytes are not elevated. Thus, the thymoproteasome optimizes CD8⁺ T cell development by supporting positive selection in the cortex independent of negative selection. The impaired generation of CD8⁺ T cells in β5t-deficient thymus is primarily due to impaired positive selection in the cortex. (D) How does the thymoproteasome work? The thymoproteasome expressed in WT cTECs produces MHC-I-associated peptides (red) that may possess structural advantage to interact with MHC-I-restricted TCR structures (for example, TCRα#1-containing TCRs as described in Section 3.3) that are preferentially used in efficiently induce positive selection of CD8⁺ T cells. However, MHC-I-associated peptides (green) displayed by β5t-knockout (KO) cTECs, which are produced independent of the thymoproteasomes, may lack such structural advantage and fail to induce to positive selection of CD8⁺ T cells.