Antigen Processing and Presentation
Cell mediated immunity (CMI) is an immune response mediated in part by CD4+ and CD8+ T cells. In order for
an immune response to be generated against a foreign antigen, the antigen must be processed into peptide
fragments then presented to T cells (via MHC molecules) by APCs (dendritic cells, macrophages, B cells).
APCs
- Capture, process, and present antigens to T cells, resulting in activation and proliferation of T cells
- Three major types of APCs
 Dendritic cells
o Located in tissues throughout the body
o Capture antigen in peripheral tissues and migrate to regional LNs
 Antigen processing occurs during migration
 Maturation of APC (more efficient at antigen presentation) occurs during migration
o DCs initiate the immune response by presenting antigen to naïve T cells
o Can also present antigen to differentiated effector and memory T cells
 Macrophages
o Phagocytose large extracellular antigens (e.g. bacteria)
o Process and present antigens to primarily differentiated effector T cells
 B cells
o BCRs bind and internalize soluble protein antigen
o Process and present antigen primarily to differentiated effector T cells
o The APC function of B cells is essential for Th cell-dependant antibody production
- Although APCs utilize different mechanisms to acquire antigen in peripheral tissues, they use common
pathways to process and present antigen to T cells
MHC Class I Antigen Processing and Presentation
- All nucleated cells express MHC class I molecules and are capable of presenting antigen to naïve effector
CD8+ T cells via the MHC class I pathway, though dendritic cells are primarily responsible
- Antigens are generally acquired in the intracellular environment (usually are viruses)
- Other proteins can be presented (e.g. mutated proteins within the cytosol of neoplastic cells)
 Thus, the MHC class I–antigen peptide complex allows CD8+ T cells to “see inside” virus-infected
cells, recognize foreign antigen, and kill the cell
- Steps of MHC class II antigen presentation
 Production of proteins in the cytosol
o Peptides presented in this pathway are derived from cytosolic proteins
 Senescent normal proteins, mutated proteins associated with neoplastic transformation,
viral proteins, or proteins derived from other intracellular pathogens
 Proteolytic degradation
o Cytosolic proteins are degraded into peptides by a proteosome
 Shaped like a large cylinder
 Large enzyme complex with a broad range of cytosolic proteolytic activity
 Proteins targeted for proteosomal degradation are polyubiquitinated in cell cytoplasm
 After ubiquitination, proteins are unfolded, ubiquitin removes, proteins threaded
through a proteosome, and chopped into 6-30 amino acid residues
 Transport of peptides from the cytosol to the ER
o Peptides generated in the cytosol are translocated to the ER by a specialized transporter
 TAP transporter (transporter associated with antigen processing)
o In the ER, newly-synthesized MHC class I molecules are able to bind to peptides
 Assembly of MHC class I–peptide complexes
o Class I α chains and β2 microglobulin are synthesized in the ER
o Antigen peptide enters the ER via the TAP transporter and binds to the peptide binding groove
of the MHC class I molecule
o MHC class I–peptide complex exits the ER

Surface expression of MHC class I–antigen peptide complexes
o MHC class I–peptide complex is transported to the cell surface via golgi and exocytic vesicles
o MHC class I molecules with bound peptides are structurally stable, expressed on the cell
surface, and able to be recognized by antigen-specific CD8+ T cells
MHC Class II Antigen Processing and Presentation
- Generally, APCs uniquely express MHC class II molecules
- Antigens are acquired in the extracellular environment, processed and presented to CD4+ cells
- Steps of MHC class II antigen presentation
 APC uptake of extracellular antigen into endosomes
o MHC class II peptides are typically derived from protein antigens that are captured in the
extracellular environment and internalized by endosomes of APCs
o Cytoplasmic and membrane proteins can enter the MHC class II pathway though will not
activate T cells because of “self recognition”
 Occurs in autophagy, turnover of cytoplasmic compartments
 Processing of internalized proteins in endolysosomes
o After antigen internalization, endosomes acidify and fuse with a lysosome to form an
endolysosome
o Proteolytic enzymes from the lysosome cleave the protein antigen into peptides 10-30 amino
acids in length
 Biosynthesis and transport of MHC class II molecules to endolysosomes
o The α and β chains of class II molecules are synthesized and associate w/ each other in the ER
o The newly-synthesized molecules associate with a protein called invariant chain (Ii)
 Located in the peptide-binding groove of the newly-made class II molecules
o MHC–Ii association prevents binding of antigen with MHC class II molecules the ER
 Instead, protein antigens bind to MHC class I molecules
o MHC class II molecule with Ii travel to the endolysosome via a vesicle
 Association of processed peptides with class II MHC molecules in vesicles
o Vesicle containing the MHC class II molecules fuse with the endolysosome
o Ii is removed from the MHC proteolytically, leaving a fragment called CLIP (class II
associated invariant chain peptide) bound to the MHC class II groove
o Within the endolysosome, a molecule called HLA-DM (or H-2M) helps remove CLIP and
facilitates loading of the antigenic peptide into the binding groove of the MHC II molecule
 Expression of MHC class I–antigen peptide complexes on the cell surface
o MHC class II molecules are stabilized by the bound peptides and the complex is delivered to
the APC cell surface where they are displayed for recognition by CD4+ T cells
 T cells are quite sensitive to antigenic stimulation and only require recognition of a few antigen
peptide-MHC molecules (~100) for activation of an immune response. This required number only
represents 0.1% of the total number of class II MHC molecules present on the APC surface
Antigen Cross-presentation
- A hybrid of MHC class I and MHC class II antigen presentation pathways
 Dendritic cells acquire extracellular antigen, process it via the endolysosome pathway, but display
resultant peptides on MHC class I molecules
- Extremely important function that allows the immune system to present extracellular pathogens to CD8+ cells
Viruses strive to replicate and spread to the next victim before killing the host. The immune system strives to
prevent both the killing of the host and spread of the virus via MHC-driven antigen peptide presentation. Some
viral peptides evoke a powerful immune response and are known as immunodominant peptides. Only certain
individuals in a population express the MHC molecules that bind to these immunodominant peptides, individuals
that mount the most robust immune response and have the best chance for survival during a pandemic.
Introduction to T Cells
- T cells can be broadly divided into two types
 CD 4+ T cells – Th cells
o Secrete cytokines to stimulate an immune response
o Promote activation of other immune cells (NK cells, macrophages, B cells)
o Support the activation and expansion of CD8+ T cells
 CD8+ T cells – Tc cells
o Kill other infected or neoplastic cells by secretion of lytic substances (perforin, granzymes)
o Produce cytokines that promote the activation of NK cells and macrophages
Differences in Antigen Specificity Between T and B Cells
B cells
Recognize peptides, nucleic acids, lipids, and carbohydrates
Recognize antigens in tertiary (folded) structure
Can bind soluble antigen
-
T cells
Only recognize peptides
Recognize amino acid sequences of peptides
Recognize and respond to antigen only when they are
presented by the MHC on the APC
TCR structure
 Heterodimer composed of two glycoprotein (α and β) chains
 Each TCR chain is encoded by multiple gene segments that undergo somatic rearrangements during the
maturation of the T cell to generate diversity (similar to what occurs with antibodies)
 Has both a hydrophobic transmembrane region and short cytoplasmic region
 Extracellular portion contains both variable (V) and constant (C) regions
o Resembles a Fab fragment of an antibody
o V regions
 Short stretches of amino acids that are highly variable between TCRs
 Form hypervariable or complementary determining regions (CDRs 1, 2, 3)
 CDRs form the part of the TCR that specifically recognize MHC–peptide complexes
o C regions
 CD4 and CD8 chains
o Co-receptors whose expression on T cells helps distinguish T cells
o Act as signal transducers that activate intracellular protein cascades once the MHC molecule–
peptide complex is bound to the TCR
o Extracellular portions of these molecules bind to invariant portion of MHC molecules on the
surface of cells that present antibody to T cells (act as adhesion molecules)
 CD4 interacts with cells expressing antigen and MHC class II (invariant β2 region)
 CD8 interacts with cells expressing antigen and MHC class I (invariant α3 region)
o Expression of CD4+ is typically double that of CD8+
 CD3
o A molecule associated with the TCR receptor and only expressed on the surface of T cells
o Acts as a signal transducer, where TCR antigen recognition causes changes in CD3 that result
in T cell activation
o Composed of three protein chains: γ, δ, ε
 Zeta (ζ) chains
o Associated with the TCR
o Acts as a signal transducer that stimulates T cell activation and proliferation
Structural Differences Between Antigen Receptors on T cells and B cells
B cells Surface Antibody Molecule
Composed of heavy and light chains
Secreted
Somatic hypermutation
Isotype switching
TCR
Composed of α and β chains
Not secreted
No somatic hypermutation
No isotype switching