Generation of their clonal TCR is the first step in T cell development

In the thymus the T cell precursors – also called thymocytes – start to express the recombinase-activating gene (RAG) products and begin to rearrange their αβ TCR genes. T cell precursors that enter the thymus express neither CD4 nor CD8 and are, therefore, called double negative (DN) thymocytes. The DN precursors actively proliferate, undergoing approximately 20 cell divisions and assemble the TCR β chain. Only those DN cells that have successfully rearranged a TCR β chain will progress to the next stage and express CD4 and CD8 simultaneously. These immature CD4⁺CD8⁺ double positive (DP) thymocytes start to reassemble TCR α chains and express T cell receptors (TCR). The randomly rearranged TCRs expressed by the DP thymocytes collectively constitute the organism’s unselected TCR repertoire which is also called the germline repertoire. These thymocytes undergo processes of positive and negative selection. Less than 5% of them survive these selection events and are allowed to exit the thymus as naive mature T cells.

In addition to αβ T cells, other lineages including natural killer T (NKT) cells and γδ T cells also develop in the thymus. Although much less is known about thymic selection of γδ T cells there are profound differences in the thymic development of γδ T cells and αβ T cells. Ligand mediated selection events do not seem to be required for the selection of the γδ T cell repertoire. In contrast, instruction for particular effector functions occurs in the thymus for γδ T cells. Given the many current uncertainties about γδ T cell selection and NKT selection in the thymus, this section will deal exclusively with thymic selection of αβ T cells.

Thymocytes are positively selected for their ability to interact with self MHC molecules

The DP T cells interact with thymic cortical epithelial cells that present peptides derived from endogenous proteins bound to major histocompatibility complex (MHC) molecules. Recognition of self-peptide/MHC complexes is vital for the DP T cells for two reasons:

Moreover, recognition of a peptide/MHC complex via the TCR is necessary for the DP T cell to receive a survival signal. This is called positive selection (see Fig 19.2). Experiments have shown that T cells are positively selected by interaction with self-MHC to prepare them for subsequent activation by non-self-peptide/self-MHC complexes, indicating the biological benefit of positive selection.

Accordingly mice that do not express MHC-class II molecules lack CD4⁺ T cells and mice that do not express MHC-class I molecules lack CD8⁺ T cells.

Positive selection occurs predominantly in the thymic cortex

Specialized APC, the cortical thymic epithelial cells (cTECs) are pivotal for positive selection. cTECs differ in their antigen processing machinery (cathepsins, proteasome subunits) from hematopoietic antigen presenting cells. Given that the number of different peptides that can be presented by any particular MHC molecule is much smaller than the number of different TCRs that undergo positive selection, each peptide must be involved in positively selecting many different T cells. Accordingly, experiments have demonstrated that the peptide on which a TCR is positively selected does not need to share sequence similarity with the peptides recognized by that same TCR in the periphery.

Note that positive selection depends on the recognition of self-peptides bound to self-MHC. The TCRs that are positively selected based on low-affinity interactions with self-peptide/MHC form the selected repertoire that ultimately recognizes microbial antigens, to protect the organism from infectious diseases. This is one illustration for the flexibility of antigen recognition by T cells. The peptides that mediate positive selection in the thymus are also presented outside the thymus where they support survival of mature T cells and may also act as co-agonists that enhance T cell activation by agonist peptides.

An immediate question is why T cells which were selected based upon self-recognition usually do not cause damage to the organism. One answer is that the threshold for TCR signaling is lower in immature DP T cells in the thymus than in mature T cells in the periphery. Thus, DP T cells can respond to low-affinity interaction with peptide/MHC complexes that would not trigger mature T cells. One important regulator of this TCR signaling threshold is the microRNA miR-181a that regulates the expression of several phosphatases involved in TCR signaling. DP T cells express much higher levels of miR181a than mature SP T cells.

Lack of survival signals leads to death by neglect

DP T cells whose receptors have a very low affinity for the peptide/MHC complexes they encounter during their approximately 3–4-day lifespan in the thymic cortex do not receive survival signals and undergo apoptosis in the thymus (see Fig. 19.w2). This is called death by neglect. Accordingly, T cells do not progress beyond the DP stage in mice that have been manipulated to lack expression of MHC molecules. Analyses of the germ line repertoire of TCRs have revealed that this unselected repertoire contains more self-MHC reactive TCRs than expected by chance. In other words: co-evolution of TCR and MHC molecules has shaped the germline αβ TCR repertoire to favor the generation of receptors that can interact with self-MHC.

Fig. 19.w2 The correlation between avidity and thymocyte selection

The avidity of a T cell’s interaction with antigenic peptide presented by an APC will depend on the level of expression of the MHC–peptide complex [MHC + peptide] on the APC and both the affinity and surface expression of TCR on the T cell. [MHC + peptide] depends on the affinity of peptide for MHC and the stability of the complex once formed. Current evidence suggests that CD25⁺ regulatory T cells are selected in the thymus and have a relatively high affinity for MHC and peptide.

Thymocytes are negatively selected if they bind strongly to self-peptides on MHC molecules

After positive selection and commitment to the CD4 or CD8 lineage in the thymic epithelium, thymocytes express the chemokine receptor CCR7 and migrate towards the central region of the thymus, the thymic medulla, where the CCR7 ligands CCL19 and CCL20 are produced. In the thymic medulla the thymocytes are probed for another 4–5 days. T cells whose receptors have a high affinity for the peptide/MHC complexes encountered in the medulla are autoreactive and therefore, potentially dangerous. They receive death signals and undergo apoptosis. This is called negative selection (see Fig 19.2). Experimental evidence suggests that the majority of the DP T cells which were positively selected are later eliminated by negative selection.

The relevance of negative thymic selection can be demonstrated by neonatal thymectomy. Mice that are thymectomized within the first three days after birth develop an autoimmune syndrome including sialadenitis, diabetes, autoimmune gastritis and hepatitis.

A library of self antigens is presented to developing T cells in the thymus

The induction of central tolerance requires the presence of autoantigens in the thymus. This poses an obvious problem for thymic selection: Some autoantigens, e.g. insulin are expressed in a tissue-specific manner, are frequently called tissue-restricted antigens (TRAs). The question, then, is (how) do TRAs get into the thymus for presentation to developing T cells? Some might be brought into the thymus by immigrating antigen presenting cells but it is highly unlikely that this would yield a reliable representation of the organism’s TRAs. Moreover, developmentally regulated TRAs, e.g. antigens that are only expressed after puberty, would not gain access to the fetal thymus. The answer is that specialized cells in the thymus, the medullary thymic epithelial cells (mTECs) express proteins that are otherwise strictly tissue restricted. This has been called ectopic or promiscuous gene expression (Fig. 19.3).

Fig 19.3 Medullary thymic epithelial cells express and present tissue restricted antigens

Different antigen presenting cell populations induce thymic tolerance. Dendritic cells and other conventional APCs present phagocytosed or endogenously synthesized proteins to T lymphocytes. T cells that express receptors with high affinity for these ubiquitous proteins will undergo apoptosis. Medullary thymic epithelial cells (mTECs) express the transcriptional autoimmune regulator, AIRE and, therefore, possess the unique capacity of expressing tissue restricted antigens (TRAs) ectopically in the thymus. This allows for intrathymic clonal deletion of T cells expressing TCRs with high affinities for antigens that are expressed in a tissue restricted manner outside the thymus.

(Adapted from Sprent J, Surh CD. Nature Immunol 2003;4:303–304.)

MTECS express several hundreds or even thousands of functionally and structurally highly diverse antigens that represent almost all tissues in the body. Importantly, mTECs express not only tissue restricted antigens but also developmentally regulated antigens. Thus, gene expression in mTECs is uncoupled from spatial and developmental regulation. The exact mechanisms of this promiscuous gene expression are not yet fully understood. It has become clear that not all mTECs express all TRAs. Any particular TRA is expressed by less than 5% of mTECs.

Whereas mTECs are the only cells known to be capable of promiscuous gene expression, they are not the only cells important for negative selection. Thymic dendritic cells can take up TRAs expressed by mTECs and cross-present these TRAs to T cells. Recent intravital imaging studies have yielded the estimate that a thymocyte makes contact with approximately 500 dendritic cells during its sojourn in the thymic medulla. Although we do not have experimentally based quantitative estimates for thymocyte:mTEC contacts, the purging of self-reactive T cells in the thymic medulla is a remarkable achievement.

Subtle quantitative alterations in the thymic expression of TRAs can be consequential. Murine intrathymic expression levels of autoantigens including insulin and myelin antigens correlate inversely with susceptibility to autoimmune diseases, type I diabetes and experimental autoimmune encephalitis (EAE) respectively. Similarly, in humans genetic variants resulting in low levels of intrathymic insulin-expression are strongly associated with susceptibility to type I diabetes.

Qualitative variations in TRAs expressed in mTECs have also been associated with autoimmune disease models. Differential splicing or the expression of embryonic, rather than mature variants of myelin autoantigens have been associated with strain-specific susceptibility to EAE and may well play a role in the pathogenesis of multiple sclerosis in humans.

AIRE controls promiscuous expression of genes in the thymus

What enables mTECs to express a broad array of TRAs independently of spatial or developmental regulation? mTECs express the transcriptional regulator Aire (autoimmune regulator). Aire controls the expression of a large number of TRAs in mTECs (see Fig. 19.3).

Similarly, in humans, point mutations in the gene coding for Aire are the cause of the rare monogenic autosomal recessive autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED) syndrome. APECED is characterized by high titres of several different autoantibodies that cause disease, mainly in endocrine organs. Together these findings strongly suggest that the autoimmune manifestations are caused by diminished expression of TRAs in thymic mTECs due to the Aire deficiency. Aire associates with a large number of partners to form distinct complexes that impinge on different steps of transcription. The different functions of Aire’s partner proteins include chromatin structure and DNA-damage response, gene transcription, RNA processing, and nuclear transport. It is still unclear, however, how Aire controls promiscuous gene expression. Moreover, experimental evidence strongly suggests that additional yet unidentified transcriptional regulators must also be involved in promiscuous gene expression by mTECs.

Immunological ignorance occurs if T cells do not encounter their cognate antigen

Immunological ignorance is maintained as long as autoreactive T-lymphocytes do not enter the tissue in which the autoantigen that they recognize is expressed. The autoreactive naive T cells are not tolerized and can be activated upon recognizing their cognate antigen.

The importance of immunological ignorance was demonstrated in mice that express a transgene-encoded TCR which recognizes a peptide derived from the lymphocytic choriomeningitis virus (LCMV). These mice were bred with another transgenic strain that expressed the viral peptide on the surface of their pancreatic islet cells. Surprisingly, diabetes did not develop in the offspring even though in vitro their T cells could kill cells that displayed the viral peptide (Fig. 19.4). The T cells in these double-transgenic mice were therefore, not tolerant in vivo, instead they were ignorant of their target cells.

Fig 19.4 Immunological ignorance

Immunological ignorance was first demonstrated in transgenic mice. (1) One transgenic strain of mice expresses a viral (LCMV) antigen under the control of the rat insulin promotor (RIP) in pancreatic islets cells. These mice remain healthy. (2) Another strain expresses a transgenically encoded T cell receptor specific for the LCMV antigen (LCMV TCR). These mice also remain healthy. (3) F1 mice from a cross between the RIP-LCMV and LCMV TCR mice express the viral antigen in the pancreas and they have T cells that express the transgenic LCMV-specific TCR. The transgenic T cells are not deleted in the thymus of these mice and they respond appropriately to LCMV antigen in vitro but, the mice remain healthy, indicating that the naive LCMV-specific T cells do not get in contact with the LCMV antigen which is expressed in the pancreas. (4) When the F1 mice are infected with LCMV, the LCMV-specific T cells become activated in the secondary lymphatic organs by high concentrations of processed antigen and can then enter the pancreas and destroy the insulin synthesizing cells. Consequently, the mice succumb to immune mediated diabetes.

When the mice were infected with LCMV, the transgenic T cells became activated, invaded the pancreas and destroyed the islet cells. Consequently the mice succumbed to diabetes. Importantly, LCMV-infection did not cause diabetes in those mice that expressed the transgenic TCR but not the LCMV-peptide in the pancreas. Once activated by LCMV infection, the hitherto ignorant autoreactive T cells (autoreactive because the LCMV-derived peptide was transgenically expressed in the pancreas) acquired the capacity to migrate into their target tissue where they recognized and destroyed the LCMV-peptide expressing islet cells (see Fig. 19.4).

Self-reactive T cells and experimental autoimmunity

Mice that express a transgene-encoded TCR specific for a myelin antigen do not develop experimental autoimmune encephalitis (EAE, a mouse model for multiple sclerosis) spontaneously although more than half of their mature naive peripheral CD4⁺ T cells express the transgene-encoded TCR. Only upon immunization with myelin antigen in adjuvant do the mice develop EAE. This system can be probed even further. When the MBP-TCR transgenic mice are bred with RAG deficient mice, all T cells in the MBP-TCR⁺RAG^−/− mice express the transgene-encoded autoreactive TCR. Even then autoimmunity does not develop spontaneously as long as the mice are not immunized with the self antigen and are kept under sterile conditions.

Lymphocyte activation enhances their migration into non-lymphoid tissues

Upon activation in secondary lymphatic organs naive T cells acquire effector functions and express a different set of chemokine receptors and adhesion molecules which then enables them to enter other organs, particularly in the context of inflammation. Naive T cells lacking those surface molecules, however, are excluded from non-lymphoid tissues so that under normal conditions, potentially autoreactive T cells will ignore their antigens, thereby maintaining self-tolerance. Should such cells be activated accidentally they would pose a permanent threat to the organism. DCs that are activated during infection are likely to present not only microbial but also self-antigens. The T cells activated in this process would gain the capacity to enter tissues and thus have lost their ignorance. Consequently, additional mechanisms must ensure the maintenance of immunological self tolerance.

The amount of released self antigen critically affects sensitization

How does the immune system decide which autoreactive T cells may survive ignorantly and which need to be deleted? Antigen dose (Fig. 19.w1) and TCR avidity play a major role. One key experiment used two different strains of mice that expressed ovalbumin (OVA) specifically in the pancreas. One strain expressed OVA at low levels and the other expressed it at high levels. Only in the high-expressing strain was OVA presented to T cells in the draining lymph nodes, resulting in the deletion of adoptively transferred OVA-specific TC cells. In the low-expressing cells the OVA-specific T cells remained ignorant. Further in vitro assays revealed that the low-level OVA-expression was still sufficient to allow recognition and killing of the OVA-expressing pancreatic β cells by the OVA-specific CTL. Therefore, tissue restricted self-antigens need to be expressed at sufficiently high levels to be presented in the draining lymph nodes. These experiments also clearly showed that self-reactive T cells remain dangerous and poised to wreak havoc even if they are temporarily ignorant. In fact, destruction of pancreatic islet cells can induce the release of sufficient amounts of self-antigen to activate OVA-specific CTL in the OVA-low expressing mice.

Fig 19.w1

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