1. Antigen Presentation And Processing W. Robert Fleischmann, Ph.D. Department of Urologic Surgery University of Minnesota Medical School rfleisch@umn.edu (612) 626-5034

2. Objectives To understand the methods by which endogenous and exogenous antigens are processed and presented to the immune system on Class I and Class II MHC molecules.

3. Dirk Quinlan, age 5 months, is brought to the clinic for evaluation of skin lesions that have appeared on his face and extremities. Dirk has been plagued by frequent bacterial infections in his upper respiratory tract. What are your thoughts? What tests might you wish to request?

4. WBC count is within the normal range. WBC differential count is within the normal range. T cells and B cells respond appropriately to T cell and B cell mitogens. Evaluation of Dirk’s antibodies is normal. Culture of biopsy material from lesions grows only normal floral bacteria. What conclusions can be draw from this information? What would you wish to do next?

5. Dirk’s lesions are quite ugly and disfiguring. They exhibit necrosis. However, pathogenic bacteria are absent. What would you wish to do next?

6. T cells in Dirk’s blood are subjected to fluorescence cell sorting, using specific antibody to CD3, CD4 and CD8. A deficiency in CD8+ T cells is noted, with an excess of CD3+, CD4-, CD8- cells and CD3- cells. Isolated CD3+, CD4-, CD8- cells are further probed with antibody to  TCR. An excess number of CD3+ T cells bearing  TCR is noted. Isolated CD3- cells are further probed with antibody to CD16. An excess of CD16+ cells is noted. What are your thoughts?

7. Overview of Ag-Presentation B cells have antibodies on their surface that bind to epitopes on native antigens However, most T cells cannot interact with native antigens. Antigens must first be processed and presented to T cells in the context being bound to MHC molecules. T cell receptors on the surface of T cells recognize the antigenic peptides bound to MHC molecules. With appropriate co-stimulation and cytokine production, the T cell is activated. Unless T cell activation occurs, most adaptive immunity does not develop.

8. Role of Ag-Presenting Cells Processing of antigen is required for recognition of an antigen by T cells. Most cells in the body can present antigen with Class I MHC molecules. –This includes the presentation of foreign antigen and self-antigens. –CD8+ cytotoxic T cells recognize antigen bound to Class I. Professional antigen-presenting cells present antigen with Class II MHC molecules. –CD4+ helper T cells recognize antigen bound to Class II.

9. Professional Ag-Presenting Cells Dendritic cells are the most effective –Immature dendritic cells in peripheral tissues express low levels of Class II molecules. These cells take up and process antigen, then move to lymph nodes. –Mature dendritic cells in lymphoid tissues express high levels of Class II molecules. These cells are the primary presenters of antigen. –Constitutively express B7 and other costimulatory molecules –Present peptides, viral antigens, and allergens Macrophages –Must be activated by phagocytosis of bacteria and by cytokines to express Class II molecules –Must be activated to express costimulatory molecules –Present particulate antigens: intracellular and extracellular pathogens B cells –Constitutively express class II MHC molecules –Must be activated by antigen binding to antibody before they express costimulatory molecules –Present soluble antigens, toxins, viruses

10. Characteristics of Ag-Presenting Cells

11. Professional Ag-Presenting Cells Class II MHC Expression B7 Costimulation Factor Expression Antigens Presented Immature Dendritic Cells Constitutively express low levels Constitutive expressed Present peptides, viral antigens, allergens Mature Dendritic Cells Constitutively express high levels Constitutively expressed Present peptides, viral antigens, allergens Macrophages Must be activated by phagocytosis to express Must be activated to express Present particulate antigen, intracellular and extracellular pathogens B Cells Constitutively expressed Must be activated to express Present soluble antigens, toxins, viruses

12. Different Types of Dendritic Cells Secretes IL-12 Suppressive activity. Secretes IL-10 and IFN-  Kuby Lymphoid origin?

13. Antigen-Processing and Presentation There are different antigen processing and presentation pathways for different MHC molecules. –Cytosolic Pathway: Presentation of antigen on Class I molecules requires intracellular protein synthesis of the endogenous antigen. –Endocytic Pathway: Presentation of antigen on Class II molecules requires the endocytic uptake of exogenous antigen.

14. Cytosolic Pathway This pathway is used for presentation of endogenous antigens. Endogenous proteins are constantly being synthesized and degraded. –Some of the rapidly degraded proteins are defective ribosomal products (DRiPs) that are synthesized incorrectly. Many are degraded to amino acids but some persist in the cytosol as peptides. Some of these peptides are sampled by the immune system and presented on the cell surface bound to MHC Class I molecules.

15. Cytosolic Degradation Pathways (a)Degradation of misfolded proteins is mediated by 20S proteasome. (b)Degradation of correctly folded proteins that are targeted for degradation by ubiquitin is mediated by 26S proteasome (20S proteasome plus 19S regulatory component that may attach to either end of the 20S proteasome).

16. Cytosolic Degradation Pathways 20S proteasome is composed of 28 polypeptide subunits arranged in 4 stacked rings of 7 subunits each. –The outer two stacked rings are composed of 7 different  subunits. The inner two stacked rings are composed of 7 different  subunits, 3 of which are proteases. –Enzymatic cleavage of proteins is thought to occur within the central tube.

17. Cytosolic Degradation Pathways 26S proteasome is composed of 20S proteasome plus two 19S regulatory peptides that associate with each end.

18. Cytosolic Degradation Pathways 20 S immunoproteasome is composed of 20S proteasome but with 3 of the  subunits substituted with new IFN-  -stimulated  subunits. –Immunoproteasome shows bias towards increased cleavage after hydrophobic amino acids and reduced cleavage after acidic amino acids. This makes these peptides favored by TAP and Class I molecules.

19. Peptide Transport to the RER Peptides from the cytosolic pathway are transported from the cytosol to the rough endoplasmic reticulum (RER) where Class I molecules are synthesized. The peptides bind to a transporter protein heterocomplex (TAP1 and TAP2) that extends across the RER membrane and are held for a period of time on the lumen side before being released into the lumen. –TAP = transporter associated with antigen processing

20. TAP Function TAP1 and TAP2 form a functional dimer. Peptides move from the proteasome to TAP dimer. Peptide is moved through endoplasmic reticulum by passage through a tube in the TAP dimer. The peptide emerges on the lumen side of the ER and is ready to be attached to MHC Class I.

21. TAP Function TAP complex has an affinity for peptides of 8-16 aa. This is close to the optimal Class I binding size of 9 aa. Final trimming by an endoplasmic reticulum aminopeptidase (ERAP1) occurs in the RER lumen. ERAP1 will degrade down to 8 aa. Peptides too small for Class I binding are degraded by ERAP2. TAP complex has an affinity for peptides with a hydrophobic or basic carboxyl-terminal aa, the preferred anchor residue for MHC Class I. Thus, TAP transports peptides that have an affinity for Class I.

22. Assembly of MHC Class I Molecules MHC Class I  chain is synthesized on the RER. It becomes associated with the chaperone protein calnexin that assists in proper folding. Class I  chain then becomes associated with the  2 microglobulin chain, releasing calnexin. ERp57, tapasin, and calreticulin become associated with the Class I complex. –ERp57 (endoplasmic reticulum protein 57) –Tapasin (TAP-associated protein) brings the Class I complex close to TAP transporter) –Calreticulin (chaperone protein) The antigenic peptide is added, releasing the other factors. Insertion of the antigenic peptide into Class I groove is a signal to transit the Class I molecule to the outer surface of the cell membrane.

23. Peptides Associated with Class I There are an excess of Class I molecules in the lumen of the RER. Thus, appropriate peptides are rapidly bound to Class I molecules. Peptides that pass through TAP and that are held for binding to Class I molecules have two unique characteristics. –They are 8-10 aa in length, most commonly 9 aa. –The contain specific amino acid residues that appear to be important for binding to the peptide cleft. The carboxyterminal anchor is generally a hydrophobic aa (leucine, isoleucine, valine) but is sometimes a charged aa. There is another anchor at the second or third aa from the aminoterminus that is also generally a hydrophobic aa. Peptides unprotected by TAP are degraded.

24. Significance of Peptides Presented on Class I Degradation and presentation of peptides on Class I permits the sampling of proteins that are synthesized in a cell. Defective ribosomal products or DRiPs are proteins that are synthesized incorrectly. –DRiPs are rapidly degraded and presented on the cell surface bound to MHC Class I molecules –This permits recognition and killing of cells that have aberrant DNA and thus produce aberrant proteins. Virus-infected cells contain a distinct 20S proteasome. –This 20S proteasome is induced by IFN-  and TNF- . –The proteasome degrades and presents viral proteins on the cell surface bound to MHC Class I molecules. –This allows recognition and killing of cells that are virus infected.

25. TAP Deficiency Some individuals have been identified who have TAP deficiency. –Cannot express Class I molecules and their antigenic peptides. –Cannot defend against bacteria Perhaps because of deficiency of IFN-  activation of M  s –Overactive NK cells NK cells monitor what cells to kill or not to kill by the density of Class I molecules on their surface –Develop necrotizing granulomatous lesions on skin of face and extremities. Can be deforming Believed to be the result of overactive NK cells

26. Dirk Quinlan Tissue from Dirk’s lesions is sectioned, stained, and examined by a pathologist. It is noted that there is an overabundance of NK cells and  T cells in the tissue. What are your thoughts?

27. Dirk Quinlan Dirk is tested for the presence of TAP1 and TAP2 genes and is found to be deficient for TAP1 gene. Why has Dirk developed the necrotic lesions?

28. Dirk Quinlan Dirk’s tissue cells lack expression of MHC Class I antigens. This a variation of Bare Lymphocyte Syndrome. Without the presence of MHC Class I, Kirk’s NK cells are not inhibited from killing by the expresssion of MHC Class I. His tissue cells are being destroyed by his NK cells. Other than treatment for bacterial infections, no other treatment is currently available for Dirk. Bone marrow transplant? This won’t work because Dirk has a problem with Class I antigen expression which is on all tissue cells.

29. Endocytic Degradation Pathway Exogenous antigens are processed through the endocytic degradation pathway. The antigens are internalized into antigen presenting cells by phagocytosis or endocytosis or both. –M  s and dendritic cells internalize by phagocytosis –B cells internalize by receptor-mediated endocytosis The internalized antigens are degraded in phagolysosomes or endosomes. The antigenic peptides are associated with Class II MHC and expressed on the cell surface.

30. Schematic of Antigen Processing The endocytic processing pathway moves antigens through 3 compartments with increasing acidity and various hydrolytic enzymes. 1-3 hrs is required for antigen to be processed and presented via the endocytic pathway. –Antibody-bound antigen is internalized in early endosomes (pH 6.0-6.5), then late endosomes (pH 5.0-6.0), and finally lysosomes (pH4.5-5.0). –Somewhere in this progression, the antibody is separated from the antigen and recycled to the cell surface. –Fusion of the late endosome with the lysosome exposes the antigen to more than 40 different proteases, nucleases, glycosidases, lipases, phospholipases, and phosphatases. –Antigen is degraded to oligopeptides of 13- 18 aa. –The oligopeptides are then bound to MHC Class II molecules which blocks further enzymatic digestion. –The Class II molecules are transported to the cell surface.

31. Role of the Invariant Chain Once exogenous antigens have been degraded to peptides they need to be combined with MHC Class II molecules. MHC Class II molecules are synthesized on the RER, trimerized and combined with a trimer of membrane bound invariant chains (Ii, CD74). The invariant chain appears to have several functions. –Assists in folding of the Class II  and  chains. –Binds to the peptide-presenting site of the Class II molecules. –Assists in the transport of Class II trimers from the RER to the Golgi and from the Golgi to cytoplasmic vesicles via signals in its cytoplasmic tail.

32. Assembly of Class II Molecules The MHC Class II molecules bound to invariant chain move from the Golgi through the endocytic pathway. With this movement, proteolytic cleavage gradually digests the invariant chain, leaving a short fragment (CLIP) bound to the antigen presenting site on the Class II molecule. (CLIP = Class II-associated invariant chain peptide). Clip bound to Class II

33. Assembly of Class II Molecules A nonclassical class II MHC molecule, HLA-DM) is required to catalyze the exchange of antigenic peptide for CLIP. Another nonclassical class II MHC molecule, HLA-DO regulates the effect of HLA-DM. –HLA-DO is expressed only on B cells and in the thymus. –Unlike other class II molecules, it is not induced by IFN- . –HLA-DO binds to HLA-DM, except in very acidic conditions. This could favor expression of peptides that pass through lysosomes in B cells. Once peptide/MHC is placed on the cell surface, the binding is exceedingly tight and the peptide does not come off under physiological conditions.

34. Summary of Antigen Processing

35. A Couple of Special Cases of Antigen Presentation

36. Cross-Presentation of Exogenous Ag Sometimes APC present exogenous antigens bound to Class I molecules. This is not well understood but is believed to occur in the lumen of the RER. This may provide a selective advantage in that it would allow dendritic cells to phagocytose viruses and present viral antigens with Class I. –This causes the generation and activation of cytotoxic T cells that can kill virus-infected cells prior to the general spread of the infection.

37. Presentation of Nonpeptide Ags by CD1 Our immune system can respond to antigens that are not peptide antigens. –Glycolipids –Polysaccharides T cells bearing  TCR rather than  TCR also express the CD1 family of nonclassical Class I molecules. –T cells with  TCR are believed to be more ancient than T cells with  –5 genes (CD1A-CD1E) encode CD1a- CD1e molecules. CD1 molecules have structures very similar to Class I molecules and associate with  2 microglobulin. –For example, CD1 present glycolipids and mycolic acid from various Mycobacterium species. –Loading Ag onto CD1 appears to occur via a third, yet unidentified pathway. CD1 molecules present to cytotoxic T cells as well as to NK cells (part of innate immunity). CD1 Class I Overlap