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Gene Mayer, Ph.D
Emertius Professor of Pathology, Microbiology and Immunology
University of South Carolina



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Logo image Jeffrey Nelson, Rush University, Chicago, Illinois  and The MicrobeLibrary


To compare and contrast antigens recognized by the TCR and BCR.
To describe the pathways involved in processing endogenous and exogenous antigens.
To discuss self MHC restriction in antigen presentation to T cells
To describe the major antigen presenting cells.
To compare and contrast presentation of conventional and superantigens.
To discuss the role of positive and negative selection in the thymus in generation of self MHC restricted T cells.


Endogenous antigen
Class I antigen processing pathway
Exogenous antigen
 Class II antigen processing pathway
Invariant chain
Self MHC restriction
Positive selection
Negative selection


MHCInew.jpg (74159 bytes) Figure 1
Pathway of class I MHC restricted presentation of an endogenously synthesized antigen. An example of such an antigen would be a viral protein made in the cell as a result of infection

Comparison of BCR and TCR 

B cells and T cells recognize different substances as antigens and in a different form. The B cell uses cell surface-bound immunoglobulin as a receptor and the specificity of that receptor is the same as the immunoglobulin that it is able to secrete after activation. B cells recognize the following antigens in soluble form: 

  • Proteins (both conformational determinants and determinants exposed by denaturation or proteolysis)

  • Nucleic acids

  • Polysaccharides

  • Some lipids

  • Small chemicals (haptens)

In contrast, the overwhelming majority of antigens for T cells are proteins, and these must be fragmented and recognized in association with MHC products expressed on the surface of nucleated cells, not in a soluble form. T cells are grouped functionally according to the class of MHC molecules that associate with the peptide fragments of the protein: helper T cells recognize only those peptides associated with class II MHC molecules, and cytotoxic T cells recognize only those peptides associated with class I MHC molecules.


Antigen processing and presentation are processes that occur within a cell that result in fragmentation (proteolysis) of proteins, association of the fragments with MHC molecules, and expression of the peptide-MHC molecules at the cell surface where they can be recognized by the T cell receptor on a T cell. However, the path leading to the association of protein fragments with MHC molecules differs for class I and class II MHC. MHC class I molecules present degradation products derived from intracellular (endogenous) proteins in the cytosol. MHC class II molecules present fragments derived from extracellular (exogenous) proteins that are located in an intracellular compartment.

Antigen processing and presentation in cells expressing class I MHC

All nucleated cells express class I MHC. As shown in Figure 1, proteins are fragmented in the cytosol by proteosomes (a complex of proteins having proteolytic activity) or by other proteases. The fragments are then transported across the membrane of the endoplasmic reticulum by transporter proteins. (The transporter proteins and some components of the proteosome  have their genes in the MHC complex). Synthesis and assembly of class I heavy chain and beta2 microglobulin occurs in the endoplasmic reticulum. Within the endoplasmic reticulum, the MHC class I heavy chain, beta2microglobulin and peptide form a stable complex that is transported to the cell surface.


Antigen processing and presentation in cells expressing class II MHC

Whereas all nucleated cells express class I MHC, only a limited group of cells express class II MHC, which includes the antigen presenting cells (APC). The principal APC are macrophages, dendritic cells (Langerhans cells), and B cells, and the expression of class II MHC molecules is either constitutive or inducible, especially by interferon-gamma in the case of macrophages.

As shown in Figure 2, exogenous proteins taken in by endocytosis are fragmented by proteases in an endosome. The alpha and beta chains of MHC class II, along with an invariant chain, are synthesized, assembled in the endoplasmic reticulum, and transported through the Golgi and trans-Golgi apparatus to reach the endosome, where the invariant chain is digested, and the peptide fragments from the exogenous protein are able to associate with the class II MHC molecules, which are finally transported to the cell surface.

fig2-mhc2.jpg (91845 bytes) Figure 2
Pathway of class II MHC-restricted presentation of an exogenous antigen


Important aspects of antigen processing and presentation

  • One way of rationalizing the development of two different pathways is that each ultimately stimulates the population of T cells that is most effective in eliminating that type of antigen.

Viruses replicate within nucleated cells in the cytosol and produce endogenous antigens that can associate with class I MHC. By killing these infected cells, cytolytic T cells help to control the spread of the virus.

Bacteria mainly reside and replicate extracellularly. By being taken up and fragmented inside cells as exogenous antigens that can associate with class II MHC molecules, helper Th2 T cells can be activated to assist B cells to make antibody against bacteria, which limits the growth of these organisms.

Some bacteria grow intracellularly inside the vesicles of cells like macrophages. Inflammatory Th1 T cells help to activate macrophages to kill the intracellular bacteria.

  • Fragments of self, as well as non-self, proteins associate with MHC molecules of both classes and are expressed at the cell surface.

  • Which protein fragments bind is a function of the chemical nature of the groove for that specific MHC molecule.

fig3-tcell.jpg (77708 bytes) Figure 3
Self MHC Restriction of Th/APC Interactions
fig3-ctl.jpg (85729 bytes) Figure 4
Virus-specific CTLs from a strain A or strain B mouse lyse only syngeneic target cells infected with a specific virus. The CTLs do not lyse uninfected target cells and are not alloreactive. Further analysis has shown that the CTLs and target cells must come from animals that share class I MHC alleles in order for the target to present viral antigens to the CTLs.


In order for a T cell to recognize and respond to a foreign protein antigen, it must recognize the MHC on the presenting cell as self MHC. This is termed self MHC restriction. Helper T cells recognize antigen in context of class II self MHC. Cytolytic T cells recognize antigen in context of class I self MHC. The process whereby T cells become restricted to recognizing self MHC molecules occurs in the thymus.

The experimental systems demonstrating self MHC restriction for APC-helper T cell interactions and for class I MHC-cytotoxic T cell interactions are shown in Figures 3 and 4, respectively.

tcr-mhc.jpg (58940 bytes)  Figure 5
Differences between antigen and super antigen. Antigenic peptides are processed within the cell and presented on the cell surface in association with class II MHC molecules. They then trigger the T-cell receptor on a T lymphocyte. Superantigens are not processed but bind to the class II MHC protein and to the V beta chain of the T cell receptor. A given superantigen activates a distinct class of T cells that express a certain V beta chain.

Note: In the case of MHC II-TCR interaction with a normally processed peptide, recognition of the peptide on the MHC molecule requires V alpha, J alpha, V beta, D beta and J beta segments of the TCR. Such an interaction occurs at low frequency. In the case of MHC II-TCR interaction with an unprocessed superantigen, only a given V beta region is recognized. This clearly would occur at a much higher frequency 

Antigen Presenting Cells

The three main types of antigen presenting cells are dendritic cells, macrophages and B cells, although other cells, that express class II MHC molecules, (e.g., thymic epithelial cells) can act as antigen presenting cells in some cases.  Dendritic cells, which are found in skin and other tissues, ingest antigens by pinocytosis and transport antigens to the lymph nodes and spleen.   In the lymph nodes and spleen they are found predominantly in the T cells areas.  Dendritic cells are the most effective antigen presenting cells and can present antigens to nave (virgin) T cells.  Furthermore, they can present internalized antigens in association with either class I or class II MHC molecules (cross presentation), although the predominant pathway for internalized antigen is the class II pathway.  The second type of antigen presenting cell is the macrophage.  These cells ingest antigen by phagocytosis or pinocytosis.  Macrophages are not as effective in presenting antigen to nave T cells but they are very good in activating memory T cells.  The third type of antigen presenting cell is the B cell.  These cells bind antigen via their surface immunoglobulin and ingest antigens by pinocytosis.  Like macrophages these cells are not as effective as dendritic cells in presenting antigen to nave T cells.  B cells are very effective in presenting antigen to memory T cells, especially when the antigen concentration is low because surface immunoglobulin on the B cells binds antigen with a high affinity.


Presentation of Superantigens

Superantigens are antigens that can polyclonally activate T cells (see antigens) to produce large quantities of cytokines that can have pathological effects.  These antigens must be presented to T cells in association with class II MHC molecules but the antigen does not need to be processed.  Figure 5 compares how conventional antigens and superantigens are presented to T cells.  In the case of a superantigen, the intact protein binds to class II MHC molecules and to one or more Vβ regions of the TCR.  The antigen is not bound to the peptide binding groove of the MHC molecule or to the antigen binding site of the TCR.  Thus, any T cell that uses a particular Vβ in its TCR will be activated by a superantigen, resulting in the activation of a large numbers of T cells.  Each superantigen will bind to a different set of Vβ regions.


thymusnew.jpg (102027 bytes) Figure 6
Prethymic T cells enter the thymus rudiment and proliferate as large lymphoblasts in the sub-capsular region of the thymus. The lymphoblasts replicate resulting in a pool of cells that differentiate. Here the cells become CD8 and CD4 positive but expression is low. TCR genes are also rearranged in these cells and the products may also be expressed on the cell surface at low levels. As the cells mature, they move into the cortex where they adhere to cortical epithelial cells which are long and branched, providing a large surface area to interact with other cells. TCRs on the surfaces of thymocytes interact with the MHC molecules on the epithelial cells leading to positive selection. The cells that are not selected are subject to apoptosis and are phagocytosed by macrophages. As the thymocytes migrate further into the cortex of the thymus, the expression of CD3, CD4, CD8 and TCR increases. TCRs with self-reactivity are deleted because of contact with autoantigens presented by dendritic cells and macrophages. This leads to negative selection. Cells that express CD4 or CD8 appear and migrate to the periphery by specialized vessels in the cortico-medullar region.

THYMic education

Both Th and Tc cells are self-MHC restricted. In addition, T cells do not normally recognize self antigens. How are self MHC restricted T cells generated and why are self reacting T cells not produced? Random VDJ rearrangements in T cells would be expected to generate some T cells that can recognize non-self MHC and some T cells that can recognize self antigens. It is the role of the thymus to ensure that the only T cells that get to the periphery are self-MHC restricted and unable to react with self antigen. Functional T cells in the periphery have to recognize foreign antigens associated with self MHC, because APC or target cells present foreign antigen associated with self MHC. However, an individual does not need functional T cells in the periphery that recognize antigen (self or foreign) associated with foreign MHC. An individual especially does not want functional T cells in the periphery that can recognize self antigens associated with self MHC because they could lead to damage of healthy, normal tissues.

As a result of random VDJ recombination events occurring in immature T cells within the thymus, TCRs of all specificities are produced. Processes in the thymus determine which TCR specificities are retained. There are two sequential steps shown in Figure 6. First, T cells with the ability to bind to self MHC molecules expressed by cortical thymic epithelial cells are retained. This is known as positive selection. Those that do not bind, undergo apoptosis. Thus, T cells having a TCR that recognizes self MHC survive. Next, T cells with the ability to bind to self MHC molecules associated with self molecules expressed by thymic epithelial cells, dendritic cells and macrophages are killed. This is known as negative selection. Those that do not bind are retained. As a result of these two steps, T cells having a TCR that recognizes self MHC and foreign antigen survive. Each T cell that survives positive and negative selection in the thymus and is released into the periphery retains its specific T cell receptor.

While positive and negative selection is occurring in the thymus the immature T cells are also expressing CD4 or CD8 antigens on their surface. Initially the pre-T cell that enters the thymus is CD4-CD8-. In the thymus it becomes CD4+CD8+ and as positive and negative selection proceeds a cell becomes either a CD4+ or CD8+ cell. The commitment to become either a CD4+ or CD8+ cells depends on which class of MHC molecule the cell encounters. If a CD4+CD8+ cell is presented with a class I molecule it will down regulate CD4 and become a CD8+ cell. If a cell is presented with a class II MHC molecule it will down regulate CD8 and become a CD4+ cell (Figure 7).

Negative selection in the periphery

Positive and negative selection in the thymus is not a 100% efficient process. In addition, not all self antigens may be expressed in the thymus. Thus some self reactive T cells may get to the periphery. Thus, there are additional mechanisms that are designed to eliminate self reactive T cells in the periphery. These will be discussed in the tolerance chapter.


Since B cells are not MHC-restricted there is no need for positive selection of B cells. However, negative selection (i.e., elimination of self-reactive clones) of B cells is required. This occurs during B cell development in the bone marrow. However, negative selection of B cells is not a critical as for T cells since, in most instances, B cells require T cell help in order to become activated. Thus, if a self reactive B cell does get to the periphery it will not be activated due to lack of T cell help.


devel.jpg (73590 bytes) Figure 7
CD4- CD8- precursor thymocytes become double positive, CD4+ CD8+  cells expressing low levels of the alpha and beta chains of the T cell receptor (TCR). Positive selection for interaction with self MHC-I or MHC-II molecules occurs in the cortical epithelium. The majority of the cells are unselected and undergo apoptosis. The cells that remain either interact with MHC-I  and lose their CD4 antigen or interact with MHC-II and lose their CD8 antigen. Autoreactive cells are then removed as a result of their interaction with self antigen peptides that are presented by cells in the corticomedullary junction and the medulla of the thymus



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