1. Antigen Presentation and MHC Molecules
Microbiology 204
Antigen Presentation and MHC Molecules
Art Weiss
October 17, 2014

2. Functions of T lymphocytes
Primary defense against intracellular microbes
Activation of other cells (phagocytes, B cells)
Killing of infected cells (i.e., CTL)
Key features:
Mediated through interactions with other cells
Allows surface molecules, cytokines to act at short range (enhances specificity)
Different classes of T lymphocytes are most effective against different types of microbes
Phagocytosed (extracellular) microbes: CD4+ helper T cells stimulate antibody production, macrophages
Cytoplasmic (endogenous microbes): CD8+ CTLs kill infected cells and eliminate reservoirs of infection

3. The Challenge for T Lymphocytes
Very few lymphocytes in the body are specific for any one microbe (or antigen)
Specificity and diversity of antigen receptors: the immune system recognizes and distinguishes between antigens
The frequency of antigen responsive lymphocytes is typically 1 in 105 to 106
Lymphocytes must be able to locate microbes that enter anywhere in the body
Lymphocytes must respond to each microbe in ways that are best able to eradicate that microbe

4. Functions of APCs
Capture antigens and take them to the “correct” place
To peripheral (secondary) lymphoid organs, through which naïve lymphocytes constantly recirculate
Display antigens in a form that can be recognized by specific lymphocytes
For T cells: MHC-associated peptides (cytosolic peptides to class I, vesicular peptides to class II)
For B cells: native antigens; APCs include macrophages, follicular dendritic cells in germinal centers
Provide “second signals” for T cell activation
Costimulators and cytokines induced by microbes; ensure that T cells respond best to microbial antigens

5. APCs are Required to Present Antigenic Peptide
Fragments to T Cells
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

6. Induction of Immune Responses
Antigens (microbes) enter through interfaces with external environment
(portals of entry: skin, GI tract, respiratory tract)
Antigens are transported to peripheral lymphoid organs (lymph nodes, spleen) by professional APCs
(Dendritic Cells) or in soluble form
Lymphocytes that recirculate through the same organs locate the antigens and are activated

7. initial antigen capture collection and capture
Sites of antigen entry
Sites of
initial antigen capture
Sites of antigen
collection and capture
Abbas, Lichtman and Pillai. Cellular and Molecular Immunology, 7th edition, 2011 c
Elsevier

8. The Capture and Presentation of Protein Antigens by Dendritic Cells
Mannose receptors, FcR
C-type Lectin receptors
and Toll-like receptors
and expression of
CCR7, and upregulation of
MHC I & II, and coreceptors

9. Maturation of Dendritic Cells
Class II MHC molecules
Number T ½
~10 hr
7 X >100 hr

10. Why are Dendritic Cells the Most Efficient APCs for Initiating Immune Responses?
Location
At sites of microbe entry (epithelia)
Express receptors (CCR1,2, and 5) that recognize inflammatory chemokines
Receptors for capturing microbes
Such as mannose and C-type lectin receptors, Toll-like receptors (TLRs) and intracellular RNA and DNA sensors which function as pattern recognition receptors to activate APCs and have very active endocytic machinery
Migration to T cell zones of lymphoid organs
Role of CCR7 (ligands are Mip-3b and SLC)
Co-localize with naïve T cells
Maturation during migration
Increase levels of MHC molecules, induce costimulators (B7 molecules, CD40) and decrease endocytic capacity
Conversion from cells for antigen capture into cells for antigen presentation and T cell activation

11. Dendritic cell subsets
Immature dendritic cells capture antigens from sites of entry
Mature (activated) DCs present antigen to and activate naïve T cells in lymphoid organs
Distinct DC subsets may stimulate differentiation to different T cell subsets (Th1, Th2)
Conventional DC’s (myeloid) can be divided into epithelial (i.e., Langerhans in skin) or interstitial/dermal – long processes sample antigens at epithelial surfaces
Plasmacytoid DCs, resemble plasma cells, are located in 2o lymphoid organs and are particularly important for Type I interferon production in response to viruses
Exposure to antigen on immature DC may induce tolerance

12. Functions of Different Antigen Presenting Cells
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

13. T cell Recognition of Virus is Genetically Controlled
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

14. Self MHC Restriction of T cells
The genes that differ between strains A and B and control T cell
recognition were found to map to a locus called the MHC
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

15. What is the Major Histocompatibility Complex (MHC)?
A genetic locus discovered on the basis of transplantation
Different individuals express products of different MHC alleles and reject grafts from one another
Human MHC: HLA (human leukocyte antigens)
Mouse MHC: H2
The peptide display molecules of the immune system
Highly polymorphic.
Different alleles of MHC molecules display distinct but overlapping sets of peptides
Determines which protein antigens are recognized in different individuals
MHC molecules determine how antigens in different cellular compartments are recognized by different classes of T cells

16. MHC-Restricted Antigen Recognition by T Cells
A T lymphocyte recognizes an antigen on an antigen-presenting cell (APC) that also expresses an MHC allele that the T cell sees as “self”
Historically, the first indication that T cells recognize complex of protein (peptide) antigen bound to MHC molecules
Antigen receptors of T cells have dual specificities:
1. For peptide antigen (responsible for specificity of immune response), and
2. For polymorphic residues of self MHC molecules (responsible for MHC restriction)
T cells learn self MHC restriction during maturation in the thymus: only T cells that “see” MHC molecules in the thymus (can only be self MHC molecules) are selected to survive

17. Schematic Representation of How a TCR Recognizes the
Peptide/MHC complex (pMHC)

18. Genes of the MHC Locus

19. Features of Class I and Class II MHC Molecules
Feature Class I MHC Class II MHC
Polypeptide chain a (44-47 kD) a (32-34 kD)
b2-microglobulin (12kD) b (29-32 kD)
Polymorphic residues a1 and a2 domains a1 and b1 domains
Coreceptor a3 domain binds CD8 b2 domain binds CD4
Source of peptide Cytosol (biosyntheic pathway) Endocytic/lysosomal
pathway
Peptides bound residues residues
Nomenclature
Human HLA-A, -B, or C HLA-DR, -DQ, -DP
Mouse H-2K, H-2D, H-2L I-A, I-E
Types of APCs All nucleated Cells DCs, Macrophages,
B cells

20. Structure of Class I MHC Molecule
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

21. MHC Molecule Structures
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

22. Some important properties of MHC molecules
MHC molecules are the immune system’s mechanism for displaying peptide antigens to T lymphocytes:
Highly polymorphic genes: large number of alleles in the population
Co-dominantly expressed: each cell has six class I molecules (3 from each parent) and class II molecules (3 from each parent + some hybrid molecules)
Class I MHC molecules are expressed on all nucleated cells
Class II MHC molecules are expressed on few cells types (specialized APCs, e.g. dendritic cells; B lymphocytes, macrophages)
Stable expression of MHC molecules on cell surfaces requires the peptide cargo
MHC molecules present foreign and self peptides
Expression of Class II MHC molecules, in particular, is up-regulated by activation of the innate immune response (IFNs, etc.)

23. Amount of MHC Molecules is Affected by Inflammation
Enhancement of Class II MHC Expression by IFNg
Similar effects
on class I MHC and
the activation of
CD8 T cells.
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

24. How Peptides Bind to MHC Molecules

25. Polymorphic residues of MHC molecules
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

26. Alleles of MHC Molecules are Co-dominantly Expressed

27. Presentation of Extracellular and Cytosolic Antigens
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

28. Antigen Processing
Conversion of native antigen (globular protein) into peptides capable of binding to MHC molecules
Occurs in same cellular compartments as synthesis and assembly of MHC molecules
Determines which source of antigen generates peptides that are displayed by class I or class II MHC
Uses cellular organelles that serve basic “housekeeping” functions in most cells

29. Pathways of antigen processing
Protein antigen in cytosol (cytoplasm) --> class I MHC pathway
Protein antigen in vesicles --> class II MHC pathway
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

30. The Class I MHC Pathway of Processing
of Endogenous Cytosolic Protein Antigens
Cytoplasmic peptides are actively transported into the ER;
class I MHC molecules are available to bind peptides in the ER
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003

31. The Immunoproteasome:
Interferon g induces new subunit proteases to alter peptides presented
Spaapen and Neefjes, Nat. Immunol. 2012

32. Class I MHC Pathway of Presentation of Cytosolic Peptide Antigens
Cytosolic proteins are processed into peptides and presented in association with class I molecules
Most cytosolic peptides are derived from endogenous (e.g. viral, tumor) proteins; some may be from phagocytosed microbes, proteins enter cytosol
CD8 binds to class I MHC; therefore, CD8+ T cells recognize class I-displayed peptides
CD8+ T cells give rise to cytotoxic T lymphocytes (CTLs) that kill other cells that harbor infections or are transformed (all nucleated cells express class I MHC)
CTLs destroy cells infected with intracellular microbes and eradicate reservoirs of infection

33. The Class II MHC Pathway of Processing of
Internalized Vesicular Protein Antigens
Endocytosed proteins are cleaved into peptides in vesicles; class II
MHC molecules are available to bind the peptides in the same vesicles

34. Class II MHC Pathway of Presentation of Vesicular Peptide Antigens
Proteins ingested into endosomes/lysosomes are processed and presented in association with class II molecules
Most vesicular peptides are derived from extracellular proteins
CD4 binds to class II MHC; therefore, CD4+ T cells recognize class II-displayed peptides (only some cell types express class II MHC)
CD4+ T cells are helper cells that activate B lymphocytes and macrophages which have encountered extracellular microbes
Antibodies and macrophages attack and destroy extracellular microbes

35. How Class I- and Class II-associated Antigen Presentation
Influence the Nature of the Host T Cell Response

36. Significance of MHC-associated Antigen Presentation
MHC molecules display foreign and self peptides from the extracellular and intracellular environment
T cells survey the body for foreign (microbial) peptides
Different classes of MHC molecules present cytosolic (endogenous) and vesicular (ingested) peptides
Helper T cells and CTLs respond to the microbes that each is best able to combat
T cell receptors only recognize MHC-peptide complexes, and MHC molecules are cell surface proteins
T cells interact with other cells and not with cell-free antigens
Only peptides bind to MHC molecules
T cells recognize only proteins (natural source of peptides)
Few peptides are presented even from complex proteins
Immunodominance: few peptides bind to any MHC molecule

37. Immunodominance of Peptide Epitopes
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003
“Determinant Selection” - MHC alleles select best binding peptides and thereby select which determinants will be immunogenic in an individual.

38. The Problem for CD8 T cells
Viruses and tumors may be present in any nucleated cells; therefore, the immune system has to be able to generate CTL responses (class I-restricted) to any nucleated cell
Only some APCs, particularly DCs, are able to initiate the responses of naïve T cells
How are antigens from virus-infected or neoplastic non-APC cell types “transferred” to APCs?

39. Cross-Presentation of Antigens to CD8+ T cells
Abbas & Lichtman. Cellular and Molecular Immunology, 5th ed. W. B. Saunders 2003
Cross presentation explains how infections of non-professional APCs can
lead to the initiation of a CD8 T cell response

40. Potential Mechanisms for Cross Presentation
Mantegazza, et al., Traffic, 2013

41. Functions of APCs
Capture antigens and take them to the “correct” anatomic site
Antigens are concentrated in peripheral lymphoid organs, through which naïve lymphocytes circulate
Display antigens in a form that can be recognized by specific lymphocytes
For T cells: MHC-associated peptides (cytosolic peptides to class I, vesicular peptides to class II)
For B cells: native antigens
Provide “second signals” for T cell activation

42. APCs and Self Antigens
Normally, APCs are constantly presenting self antigens
MHC molecules do not distinguish self from foreign
If MHC molecules are bathed in self peptides, how can they ever be free to present microbial peptides?
Very few peptides (complexed with MHC) are enough to activate specific T cells
Microbes induce “second signals” on APCs
If self peptides are always being displayed, why do we not react against our own antigens?