By contrast, MHC class II molecules are expressed primarily only on cells of the immune system, and particularly by dendritic cells, macrophages, and B cells. Thymic cortical epithelial cells and activated, but not naive, T cells can express MHC class II molecules, which can also be induced on many cells in response to the cytokine IFN-γ. Thus, CD4 T cells can recognize their cognate antigens during their development in the thymus, on a limited set of ‘professional’ antigen-presenting cells, and on other somatic cells under specific inflammatory conditions. Effector CD4 T cells comprise several subsets with different activities that help eliminate the pathogens. Importantly, naive CD8 and CD4 T cells can become armed effector cells only after encountering their cognate antigen once it has been processed and presented by activated dendritic cells.
In considering antigen processing, it is important to distinguish between the various cellular compartments from which antigens can be derived (Fig. 6.1). These compartments, which are separated by membranes, include the cytosol and the various vesicular compartments involved in endocytosis and secretion. Peptides derived from the cytosol are transported into the endoplasmic reticulum and directly loaded onto newly synthesized MHC class I molecules on the same cell for recognition by T cells, as we will discuss below in greater detail. Because viruses and some bacteria replicate in the cytosol or in the contiguous nuclear compartment, peptides from their components can be loaded onto MHC class I molecules by this process (Fig. 6.2, first upper panel).
Fig. 6.1 There are two categories of major intracellular compartments, separated by membranes. One compartment is the cytosol, which communicates with the nucleus via pores in the nuclear membrane. The other is the vesicular system, which comprises the endoplasmic reticulum, Golgi apparatus, endosomes, lysosomes, and other intracellular vesicles. The vesicular system can be thought of as being continuous with the extracellular fluid. Secretory vesicles bud off from the endoplasmic reticulum and are transported via fusion with Golgi membranes to move vesicular contents out of the cell. Extracellular material is taken up by endocytosis or phagocytosis into endosomes or phagosomes, respectively. The fusion of incoming and outgoing vesicles is important both for pathogen destruction in cells such as neutrophils and for antigen presentation. Autophagosomes surround components in the cytosol and deliver them to lysosomes in a process known as autophagy.
This pathway of recognition is sometimes referred to as direct presentation, and can identify both somatic and immune cells that are infected by a pathogen.
Certain pathogenic bacteria and protozoan parasites survive ingestion by macrophages and are able to replicate inside the intracellular vesicles of the endosomal–lysosomal system (Fig. 6.2, second panel). Other pathogenic bacteria proliferate outside cells, and can be internalized, along with their toxic products, by phagocytosis, receptor-mediated endocytosis, or macropinocytosis into endosomes and lysosomes, where they are broken down by digestive enzymes. For example, receptor-mediated endocytosis by B cells can efficiently internalize extracellular antigens through B-cell receptors (Fig. 6.2, third panel). Virus particles and parasite antigens in extracellular fluids can also be taken up by these routes and degraded, and their peptides presented to T cells.